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1 # bettercallsal
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2
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3 `bettercallsal` is an automated workflow to assign Salmonella serotype based on [NCBI Pathogens Database](https://www.ncbi.nlm.nih.gov/pathogens). It uses `MASH` to reduce the search space followed by additional genome filtering with `sourmash`. It then performs genome based alignment with `kma` followed by count generation using `salmon`. This workflow is especially useful in a case where a sample is of multi-serovar mixture.
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4
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5 \
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6
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7
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8 <!-- TOC -->
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9
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10 - [Minimum Requirements](#minimum-requirements)
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11 - [Usage and Examples](#usage-and-examples)
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12 - [Database](#database)
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13 - [Input](#input)
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14 - [Output](#output)
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15 - [Computational resources](#computational-resources)
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16 - [Runtime profiles](#runtime-profiles)
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17 - [your_institution.config](#your_institutionconfig)
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18 - [Cloud computing](#cloud-computing)
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19 - [Example data](#example-data)
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20 - [Using sourmash](#using-sourmash)
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21 - [bettercallsal CLI Help](#bettercallsal-cli-help)
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22
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23 <!-- /TOC -->
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24
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25 \
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26
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27
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28 ## Minimum Requirements
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29
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30 1. [Nextflow version 22.10.0](https://github.com/nextflow-io/nextflow/releases/download/v22.10.0/nextflow).
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31 - Make the `nextflow` binary executable (`chmod 755 nextflow`) and also make sure that it is made available in your `$PATH`.
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32 - If your existing `JAVA` install does not support the newest **Nextflow** version, you can try **Amazon**'s `JAVA` (OpenJDK): [Corretto](https://corretto.aws/downloads/latest/amazon-corretto-17-x64-linux-jdk.tar.gz).
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33 2. Either of `micromamba` or `docker` or `singularity` installed and made available in your `$PATH`.
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34 - Running the workflow via `micromamba` software provisioning is **preferred** as it does not require any `sudo` or `admin` privileges or any other configurations with respect to the various container providers.
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35 - To install `micromamba` for your system type, please follow these [installation steps](https://mamba.readthedocs.io/en/latest/installation.html#manual-installation) and make sure that the `micromamba` binary is made available in your `$PATH`.
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36 - Just the `curl` step is sufficient to download the binary as far as running the workflows are concerned.
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37 3. Minimum of 10 CPU cores and about 16 GBs for main workflow steps. More memory may be required if your **FASTQ** files are big.
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38
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39 \
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40
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41
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42 ## Usage and Examples
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43
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44 Clone or download this repository and then call `cpipes`.
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45
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46 ```bash
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47 cpipes --pipeline bettercallsal [options]
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48 ```
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49
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50 \
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51
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52
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53 **Example**: Run the default `bettercallsal` pipeline in single-end mode.
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54
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55 ```bash
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56 cd /data/scratch/$USER
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57 mkdir nf-cpipes
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58 cd nf-cpipes
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59 cpipes
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60 --pipeline bettercallsal \
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61 --input /path/to/illumina/fastq/dir \
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62 --output /path/to/output \
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63 --bcs_root_dbdir /data/Kranti_Konganti/bettercallsal_db
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64 ```
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65
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66 \
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67
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68
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69 **Example**: Run the `bettercallsal` pipeline in paired-end mode. In this mode, the `R1` and `R2` files are concatenated. We have found that concatenated reads yields better calling rates. Please refer to the **Methods** and the **Results** section in our [preprint](https://www.biorxiv.org/content/10.1101/2023.04.06.535929v1.full) for more information. Users can still choose to use `bbmerge.sh` by adding the following options on the command-line: `--bbmerge_run true --bcs_concat_pe false`.
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70
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71 ```bash
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72 cd /data/scratch/$USER
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73 mkdir nf-cpipes
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74 cd nf-cpipes
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75 cpipes \
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76 --pipeline bettercallsal \
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77 --input /path/to/illumina/fastq/dir \
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78 --output /path/to/output \
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79 --bcs_root_dbdir /data/Kranti_Konganti/bettercallsal_db \
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80 --fq_single_end false \
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81 --fq_suffix '_R1_001.fastq.gz'
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82 ```
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83
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84 \
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85
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86
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87 ### Database
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88
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89 ---
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90
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91 The successful run of the workflow requires certain database flat files specific for the workflow.
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92
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93 Please refer to `bettercallsal_db` [README](./bettercallsal_db.md) if you would like to run the workflow on the latest version of the **PDG** release.
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94
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95
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96
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97 ### Input
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98
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99 ---
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100
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101 The input to the workflow is a folder containing compressed (`.gz`) FASTQ files. Please note that the sample grouping happens automatically by the file name of the FASTQ file. If for example, a single sample is sequenced across multiple sequencing lanes, you can choose to group those FASTQ files into one sample by using the `--fq_filename_delim` and `--fq_filename_delim_idx` options. By default, `--fq_filename_delim` is set to `_` (underscore) and `--fq_filename_delim_idx` is set to 1.
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102
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103 For example, if the directory contains FASTQ files as shown below:
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104
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105 - KB-01_apple_L001_R1.fastq.gz
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106 - KB-01_apple_L001_R2.fastq.gz
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107 - KB-01_apple_L002_R1.fastq.gz
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108 - KB-01_apple_L002_R2.fastq.gz
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109 - KB-02_mango_L001_R1.fastq.gz
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110 - KB-02_mango_L001_R2.fastq.gz
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111 - KB-02_mango_L002_R1.fastq.gz
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112 - KB-02_mango_L002_R2.fastq.gz
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113
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114 Then, to create 2 sample groups, `apple` and `mango`, we split the file name by the delimitor (underscore in the case, which is default) and group by the first 2 words (`--fq_filename_delim_idx 2`).
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115
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116 This goes without saying that all the FASTQ files should have uniform naming patterns so that `--fq_filename_delim` and `--fq_filename_delim_idx` options do not have any adverse effect in collecting and creating a sample metadata sheet.
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117
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118 \
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119
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120
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121 ### Output
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122
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123 ---
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124
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125 All the outputs for each step are stored inside the folder mentioned with the `--output` option. A `multiqc_report.html` file inside the `bettercallsal-multiqc` folder can be opened in any browser on your local workstation which contains a consolidated brief report.
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126
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127 \
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128
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129
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130 ### Computational resources
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131
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132 ---
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133
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134 The workflow `bettercallsal` requires at least a minimum of 16 GBs of memory to successfully finish the workflow. By default, `bettercallsal` uses 10 CPU cores where possible. You can change this behavior and adjust the CPU cores with `--max_cpus` option.
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135
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136 \
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137
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138
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139 Example:
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140
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141 ```bash
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142 cpipes \
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143 --pipeline bettercallsal \
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144 --input /path/to/bettercallsal_sim_reads \
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145 --output /path/to/bettercallsal_sim_reads_output \
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146 --bcs_root_dbdir /path/to/PDG000000002.2537
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147 --kmaalign_ignorequals \
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148 --max_cpus 5 \
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149 -profile stdkondagac \
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150 -resume
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151 ```
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152
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153 \
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154
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155
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156 ### Runtime profiles
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157
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158 ---
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159
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160 You can use different run time profiles that suit your specific compute environments i.e., you can run the workflow locally on your machine or in a grid computing infrastructure.
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161
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162 \
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163
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164
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165 Example:
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166
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167 ```bash
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168 cd /data/scratch/$USER
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169 mkdir nf-cpipes
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170 cd nf-cpipes
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171 cpipes \
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172 --pipeline bettercallsal \
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173 --input /path/to/fastq_pass_dir \
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174 --output /path/to/where/output/should/go \
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175 -profile your_institution
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176 ```
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177
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178 The above command would run the pipeline and store the output at the location per the `--output` flag and the **NEXTFLOW** reports are always stored in the current working directory from where `cpipes` is run. For example, for the above command, a directory called `CPIPES-bettercallsal` would hold all the **NEXTFLOW** related logs, reports and trace files.
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179
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180 \
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181
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182
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183 ### `your_institution.config`
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184
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185 ---
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186
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187 In the above example, we can see that we have mentioned the run time profile as `your_institution`. For this to work, add the following lines at the end of [`computeinfra.config`](../conf/computeinfra.config) file which should be located inside the `conf` folder. For example, if your institution uses **SGE** or **UNIVA** for grid computing instead of **SLURM** and has a job queue named `normal.q`, then add these lines:
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188
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189 \
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190
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191
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192 ```groovy
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193 your_institution {
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194 process.executor = 'sge'
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195 process.queue = 'normal.q'
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196 singularity.enabled = false
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197 singularity.autoMounts = true
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198 docker.enabled = false
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199 params.enable_conda = true
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200 conda.enabled = true
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201 conda.useMicromamba = true
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202 params.enable_module = false
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203 }
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204 ```
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205
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206 In the above example, by default, all the software provisioning choices are disabled except `conda`. You can also choose to remove the `process.queue` line altogether and the `bettercallsal` workflow will request the appropriate memory and number of CPU cores automatically, which ranges from 1 CPU, 1 GB and 1 hour for job completion up to 10 CPU cores, 1 TB and 120 hours for job completion.
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207
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208 \
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209
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210
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211 ### Cloud computing
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212
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213 ---
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214
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215 You can run the workflow in the cloud (works only with proper set up of AWS resources). Add new run time profiles with required parameters per [Nextflow docs](https://www.nextflow.io/docs/latest/executor.html):
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216
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217 \
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218
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219
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220 Example:
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221
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222 ```groovy
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223 my_aws_batch {
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224 executor = 'awsbatch'
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225 queue = 'my-batch-queue'
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226 aws.batch.cliPath = '/home/ec2-user/miniconda/bin/aws'
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227 aws.batch.region = 'us-east-1'
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228 singularity.enabled = false
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229 singularity.autoMounts = true
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230 docker.enabled = true
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231 params.conda_enabled = false
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232 params.enable_module = false
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233 }
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234 ```
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235
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236 \
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237
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238
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239 ### Example data
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240
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241 ---
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242
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243 After you make sure that you have all the [minimum requirements](#minimum-requirements) to run the workflow, you can try the `bettercallsal` pipeline on some simulated reads. The following input dataset contains simulated reads for `Montevideo` and `I 4,[5],12:i:-` in about roughly equal proportions.
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244
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245 - Download simulated reads: [S3](https://cfsan-pub-xfer.s3.amazonaws.com/Kranti.Konganti/bettercallsal/bettercallsal_sim_reads.tar.bz2) (~ 3 GB).
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246 - Download pre-formatted test database: [S3](https://cfsan-pub-xfer.s3.amazonaws.com/Kranti.Konganti/bettercallsal/PDG000000002.2491.test-db.tar.bz2) (~ 75 MB). This test database works only with the simulated reads.
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247 - Download pre-formatted full database (**Optional**): If you would like to do a complete run with your own **FASTQ** datasets, you can either create your own [database](./bettercallsal_db.md) or use [PDG000000002.2537](https://cfsan-pub-xfer.s3.amazonaws.com/Kranti.Konganti/bettercallsal/PDG000000002.2537.tar.bz2) version of the database (~ 37 GB).
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248 - After succesful run of the workflow, your **MultiQC** report should look something like [this](https://cfsan-pub-xfer.s3.amazonaws.com/Kranti.Konganti/bettercallsal/bettercallsal_sim_reads_mqc.html).
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249
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250 Now run the workflow by ignoring quality values since these are simulated base qualities:
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251
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252 \
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253
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254
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255 ```bash
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256 cpipes \
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257 --pipeline bettercallsal \
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258 --input /path/to/bettercallsal_sim_reads \
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259 --output /path/to/bettercallsal_sim_reads_output \
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260 --bcs_root_dbdir /path/to/PDG000000002.2537
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261 --kmaalign_ignorequals \
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262 -profile stdkondagac \
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263 -resume
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264 ```
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265
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266 Please note that the run time profile `stdkondagac` will run jobs locally using `micromamba` for software provisioning. The first time you run the command, a new folder called `kondagac_cache` will be created and subsequent runs should use this `conda` cache.
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267
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268 \
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269
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270
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271 ## Using `sourmash`
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272
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273 Beginning with `v0.3.0` of `bettercallsal` workflow, `sourmash` sketching is used to further narrow down possible serotype hits. It is **ON** by default. This will enable the generation of **ANI Containment** matrix for **Samples** vs **Genomes**. There may be multiple hits for the same serotype in the final **MultiQC** report as multiple genome accessions can belong to a single serotype.
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274
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275 You can turn **OFF** this feature with `--sourmashsketch_run false` option.
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kkonganti@1
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276
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kkonganti@1
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277 \
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kkonganti@1
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278
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kkonganti@1
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279
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kkonganti@1
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280 ## `bettercallsal` CLI Help
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281
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kkonganti@1
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282 ```text
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kkonganti@1
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283 [Kranti_Konganti@my-unix-box ]$ cpipes --pipeline bettercallsal --help
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kkonganti@1
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284 N E X T F L O W ~ version 22.10.0
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285 Launching `./bettercallsal/cpipes` [awesome_chandrasekhar] DSL2 - revision: 8da4e11078
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286 ================================================================================
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kkonganti@1
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287 (o)
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kkonganti@1
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288 ___ _ __ _ _ __ ___ ___
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kkonganti@1
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289 / __|| '_ \ | || '_ \ / _ \/ __|
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kkonganti@1
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290 | (__ | |_) || || |_) || __/\__ \
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kkonganti@1
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291 \___|| .__/ |_|| .__/ \___||___/
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kkonganti@1
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292 | | | |
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kkonganti@1
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293 |_| |_|
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kkonganti@1
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294 --------------------------------------------------------------------------------
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kkonganti@1
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295 A collection of modular pipelines at CFSAN, FDA.
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kkonganti@1
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296 --------------------------------------------------------------------------------
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297 Name : CPIPES
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298 Author : Kranti Konganti
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299 Version : 0.5.0
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kkonganti@1
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300 Center : CFSAN, FDA.
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kkonganti@1
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301 ================================================================================
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302
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kkonganti@1
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303 Workflow : bettercallsal
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kkonganti@1
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304
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kkonganti@1
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305 Author : Kranti Konganti
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kkonganti@1
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306
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kkonganti@1
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307 Version : 0.5.0
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kkonganti@1
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308
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kkonganti@1
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309
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kkonganti@1
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310 Usage : cpipes --pipeline bettercallsal [options]
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311
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kkonganti@1
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312
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kkonganti@1
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313 Required :
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kkonganti@1
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314
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kkonganti@1
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315 --input : Absolute path to directory containing FASTQ
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kkonganti@1
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316 files. The directory should contain only
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kkonganti@1
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317 FASTQ files as all the files within the
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kkonganti@1
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318 mentioned directory will be read. Ex: --
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kkonganti@1
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319 input /path/to/fastq_pass
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kkonganti@1
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320
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kkonganti@1
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321 --output : Absolute path to directory where all the
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kkonganti@1
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322 pipeline outputs should be stored. Ex: --
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kkonganti@1
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323 output /path/to/output
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kkonganti@1
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324
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kkonganti@1
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325 Other options :
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kkonganti@1
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326
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kkonganti@1
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327 --metadata : Absolute path to metadata CSV file
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kkonganti@1
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328 containing five mandatory columns: sample,
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kkonganti@1
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329 fq1,fq2,strandedness,single_end. The fq1
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kkonganti@1
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330 and fq2 columns contain absolute paths to
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kkonganti@1
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331 the FASTQ files. This option can be used in
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kkonganti@1
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332 place of --input option. This is rare. Ex
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kkonganti@1
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333 : --metadata samplesheet.csv
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kkonganti@1
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334
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kkonganti@1
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335 --fq_suffix : The suffix of FASTQ files (Unpaired reads
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kkonganti@1
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336 or R1 reads or Long reads) if an input
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kkonganti@1
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337 directory is mentioned via --input option.
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kkonganti@1
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338 Default: .fastq.gz
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kkonganti@1
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339
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kkonganti@1
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340 --fq2_suffix : The suffix of FASTQ files (Paired-end reads
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kkonganti@1
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341 or R2 reads) if an input directory is
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kkonganti@1
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342 mentioned via --input option. Default:
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kkonganti@1
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343 _R2_001.fastq.gz
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kkonganti@1
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344
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kkonganti@1
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345 --fq_filter_by_len : Remove FASTQ reads that are less than this
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kkonganti@1
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346 many bases. Default: 0
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kkonganti@1
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347
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kkonganti@1
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348 --fq_strandedness : The strandedness of the sequencing run.
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kkonganti@1
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349 This is mostly needed if your sequencing
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kkonganti@1
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350 run is RNA-SEQ. For most of the other runs
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kkonganti@1
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351 , it is probably safe to use unstranded for
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kkonganti@1
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352 the option. Default: unstranded
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kkonganti@1
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353
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kkonganti@1
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354 --fq_single_end : SINGLE-END information will be auto-
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kkonganti@1
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355 detected but this option forces PAIRED-END
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kkonganti@1
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356 FASTQ files to be treated as SINGLE-END so
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kkonganti@1
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357 only read 1 information is included in auto
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kkonganti@1
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358 -generated samplesheet. Default: true
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kkonganti@1
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359
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kkonganti@1
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360 --fq_filename_delim : Delimiter by which the file name is split
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kkonganti@1
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361 to obtain sample name. Default: _
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kkonganti@1
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362
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kkonganti@1
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363 --fq_filename_delim_idx : After splitting FASTQ file name by using
|
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kkonganti@1
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364 the --fq_filename_delim option, all
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kkonganti@1
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365 elements before this index (1-based) will
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kkonganti@1
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366 be joined to create final sample name.
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kkonganti@1
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367 Default: 1
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kkonganti@1
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368
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kkonganti@1
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369 --bcs_concat_pe : Concatenate paired-end files. Default: true
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kkonganti@1
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370
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kkonganti@1
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371 --bbmerge_run : Run BBMerge tool. Default: false
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kkonganti@1
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372
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kkonganti@1
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373 --bbmerge_reads : Quit after this many read pairs (-1 means
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kkonganti@1
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374 all) Default: -1
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kkonganti@1
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375
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kkonganti@1
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376 --bbmerge_adapters : Absolute UNIX path pointing to the adapters
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kkonganti@1
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377 file in FASTA format. Default: false
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kkonganti@1
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378
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kkonganti@1
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379 --bbmerge_ziplevel : Set to 1 (lowest) through 9 (max) to change
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kkonganti@1
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380 compression level; lower compression is
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kkonganti@1
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381 faster. Default: 1
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kkonganti@1
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382
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kkonganti@1
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383 --bbmerge_ordered : Output reads in the same order as input.
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kkonganti@1
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384 Default: false
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kkonganti@1
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385
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kkonganti@1
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386 --bbmerge_qtrim : Trim read ends to remove bases with quality
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kkonganti@1
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387 below --bbmerge_minq. Trims BEFORE merging
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kkonganti@1
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388 . Values: t (trim both ends), f (neither
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kkonganti@1
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389 end), r (right end only), l (left end only
|
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kkonganti@1
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390 ). Default: true
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kkonganti@1
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391
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kkonganti@1
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392 --bbmerge_qtrim2 : May be specified instead of --bbmerge_qtrim
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kkonganti@1
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393 to perform trimming only if merging is
|
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kkonganti@1
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394 unsuccesful. then retry merging. Default:
|
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kkonganti@1
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395 false
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kkonganti@1
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396
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kkonganti@1
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397 --bbmerge_trimq : Trim quality threshold. This may be comma-
|
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kkonganti@1
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398 delimited list (ascending) to try multiple
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kkonganti@1
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399 values. Default: 10
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kkonganti@1
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400
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kkonganti@1
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401 --bbmerge_minlength : (ml) Reads shorter than this after trimming
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kkonganti@1
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402 , but before merging, will be discarded.
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kkonganti@1
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403 Pairs will be discarded onlyif both are
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kkonganti@1
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404 shorter. Default: 1
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kkonganti@1
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405
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kkonganti@1
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406 --bbmerge_tbo : (trimbyoverlap). Trim overlapping reads to
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kkonganti@1
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407 remove right most (3') non-overlaping
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kkonganti@1
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408 portion instead of joining Default: false
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kkonganti@1
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409
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kkonganti@1
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410 --bbmerge_minavgquality : (maq). Reads with average quality below
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kkonganti@1
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411 this after trimming will not be attempted
|
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kkonganti@1
|
412 to merge. Default: 30
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kkonganti@1
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413
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kkonganti@1
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414 --bbmerge_trimpolya : Trim trailing poly-A tail from adapter
|
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kkonganti@1
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415 output. Only affects outadapter. This also
|
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kkonganti@1
|
416 trims poly-A followed by poly-G, which
|
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kkonganti@1
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417 occurs on NextSeq. Default: true
|
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kkonganti@1
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418
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kkonganti@1
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419 --bbmerge_pfilter : Ban improbable overlaps. Higher is more
|
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kkonganti@1
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420 strict. 0 will disable the filter; 1 will
|
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kkonganti@1
|
421 allow only perfect overlaps. Default: 1
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kkonganti@1
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422
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kkonganti@1
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423 --bbmerge_ouq : Calculate best overlap using quality values
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kkonganti@1
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424 . Default: false
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kkonganti@1
|
425
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kkonganti@1
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426 --bbmerge_owq : Calculate best overlap without using
|
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kkonganti@1
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427 quality values. Default: true
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kkonganti@1
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428
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kkonganti@1
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429 --bbmerge_strict : Decrease false positive rate and merging
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kkonganti@1
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430 rate. Default: false
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kkonganti@1
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431
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kkonganti@1
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432 --bbmerge_verystrict : Greatly decrease false positive rate and
|
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kkonganti@1
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433 merging rate. Default: false
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kkonganti@1
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434
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kkonganti@1
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435 --bbmerge_ultrastrict : Decrease false positive rate and merging
|
|
kkonganti@1
|
436 rate even more. Default: true
|
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kkonganti@1
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437
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kkonganti@1
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438 --bbmerge_maxstrict : Maxiamally decrease false positive rate and
|
|
kkonganti@1
|
439 merging rate. Default: false
|
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kkonganti@1
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440
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kkonganti@1
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441 --bbmerge_loose : Increase false positive rate and merging
|
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kkonganti@1
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442 rate. Default: false
|
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kkonganti@1
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443
|
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kkonganti@1
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444 --bbmerge_veryloose : Greatly increase false positive rate and
|
|
kkonganti@1
|
445 merging rate. Default: false
|
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kkonganti@1
|
446
|
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kkonganti@1
|
447 --bbmerge_ultraloose : Increase false positive rate and merging
|
|
kkonganti@1
|
448 rate even more. Default: false
|
|
kkonganti@1
|
449
|
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kkonganti@1
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450 --bbmerge_maxloose : Maximally increase false positive rate and
|
|
kkonganti@1
|
451 merging rate. Default: false
|
|
kkonganti@1
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452
|
|
kkonganti@1
|
453 --bbmerge_fast : Fastest possible preset. Default: false
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kkonganti@1
|
454
|
|
kkonganti@1
|
455 --bbmerge_k : Kmer length. 31 (or less) is fastest and
|
|
kkonganti@1
|
456 uses the least memory, but higher values
|
|
kkonganti@1
|
457 may be more accurate. 60 tends to work well
|
|
kkonganti@1
|
458 for 150bp reads. Default: 60
|
|
kkonganti@1
|
459
|
|
kkonganti@1
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460 --bbmerge_prealloc : Pre-allocate memory rather than dynamically
|
|
kkonganti@1
|
461 growing. Faster and more memory-efficient
|
|
kkonganti@1
|
462 for large datasets. A float fraction (0-1)
|
|
kkonganti@1
|
463 may be specified, default 1. Default: true
|
|
kkonganti@1
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464
|
|
kkonganti@1
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465 --fastp_run : Run fastp tool. Default: true
|
|
kkonganti@1
|
466
|
|
kkonganti@1
|
467 --fastp_failed_out : Specify whether to store reads that cannot
|
|
kkonganti@1
|
468 pass the filters. Default: false
|
|
kkonganti@1
|
469
|
|
kkonganti@1
|
470 --fastp_merged_out : Specify whether to store merged output or
|
|
kkonganti@1
|
471 not. Default: false
|
|
kkonganti@1
|
472
|
|
kkonganti@1
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473 --fastp_overlapped_out : For each read pair, output the overlapped
|
|
kkonganti@1
|
474 region if it has no mismatched base.
|
|
kkonganti@1
|
475 Default: false
|
|
kkonganti@1
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476
|
|
kkonganti@1
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477 --fastp_6 : Indicate that the input is using phred64
|
|
kkonganti@1
|
478 scoring (it'll be converted to phred33, so
|
|
kkonganti@1
|
479 the output will still be phred33). Default
|
|
kkonganti@1
|
480 : false
|
|
kkonganti@1
|
481
|
|
kkonganti@1
|
482 --fastp_reads_to_process : Specify how many reads/pairs are to be
|
|
kkonganti@1
|
483 processed. Default value 0 means process
|
|
kkonganti@1
|
484 all reads. Default: 0
|
|
kkonganti@1
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485
|
|
kkonganti@1
|
486 --fastp_fix_mgi_id : The MGI FASTQ ID format is not compatible
|
|
kkonganti@1
|
487 with many BAM operation tools, enable this
|
|
kkonganti@1
|
488 option to fix it. Default: false
|
|
kkonganti@1
|
489
|
|
kkonganti@1
|
490 --fastp_A : Disable adapter trimming. On by default.
|
|
kkonganti@1
|
491 Default: false
|
|
kkonganti@1
|
492
|
|
kkonganti@1
|
493 --fastp_adapter_fasta : Specify a FASTA file to trim both read1 and
|
|
kkonganti@1
|
494 read2 (if PE) by all the sequences in this
|
|
kkonganti@1
|
495 FASTA file. Default: false
|
|
kkonganti@1
|
496
|
|
kkonganti@1
|
497 --fastp_f : Trim how many bases in front of read1.
|
|
kkonganti@1
|
498 Default: 0
|
|
kkonganti@1
|
499
|
|
kkonganti@1
|
500 --fastp_t : Trim how many bases at the end of read1.
|
|
kkonganti@1
|
501 Default: 0
|
|
kkonganti@1
|
502
|
|
kkonganti@1
|
503 --fastp_b : Max length of read1 after trimming. Default
|
|
kkonganti@1
|
504 : 0
|
|
kkonganti@1
|
505
|
|
kkonganti@1
|
506 --fastp_F : Trim how many bases in front of read2.
|
|
kkonganti@1
|
507 Default: 0
|
|
kkonganti@1
|
508
|
|
kkonganti@1
|
509 --fastp_T : Trim how many bases at the end of read2.
|
|
kkonganti@1
|
510 Default: 0
|
|
kkonganti@1
|
511
|
|
kkonganti@1
|
512 --fastp_B : Max length of read2 after trimming. Default
|
|
kkonganti@1
|
513 : 0
|
|
kkonganti@1
|
514
|
|
kkonganti@1
|
515 --fastp_dedup : Enable deduplication to drop the duplicated
|
|
kkonganti@1
|
516 reads/pairs. Default: true
|
|
kkonganti@1
|
517
|
|
kkonganti@1
|
518 --fastp_dup_calc_accuracy : Accuracy level to calculate duplication (1~
|
|
kkonganti@1
|
519 6), higher level uses more memory (1G, 2G,
|
|
kkonganti@1
|
520 4G, 8G, 16G, 24G). Default 1 for no-dedup
|
|
kkonganti@1
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521 mode, and 3 for dedup mode. Default: 6
|
|
kkonganti@1
|
522
|
|
kkonganti@1
|
523 --fastp_poly_g_min_len : The minimum length to detect polyG in the
|
|
kkonganti@1
|
524 read tail. Default: 10
|
|
kkonganti@1
|
525
|
|
kkonganti@1
|
526 --fastp_G : Disable polyG tail trimming. Default: true
|
|
kkonganti@1
|
527
|
|
kkonganti@1
|
528 --fastp_x : Enable polyX trimming in 3' ends. Default:
|
|
kkonganti@1
|
529 false
|
|
kkonganti@1
|
530
|
|
kkonganti@1
|
531 --fastp_poly_x_min_len : The minimum length to detect polyX in the
|
|
kkonganti@1
|
532 read tail. Default: 10
|
|
kkonganti@1
|
533
|
|
kkonganti@1
|
534 --fastp_cut_front : Move a sliding window from front (5') to
|
|
kkonganti@1
|
535 tail, drop the bases in the window if its
|
|
kkonganti@1
|
536 mean quality < threshold, stop otherwise.
|
|
kkonganti@1
|
537 Default: true
|
|
kkonganti@1
|
538
|
|
kkonganti@1
|
539 --fastp_cut_tail : Move a sliding window from tail (3') to
|
|
kkonganti@1
|
540 front, drop the bases in the window if its
|
|
kkonganti@1
|
541 mean quality < threshold, stop otherwise.
|
|
kkonganti@1
|
542 Default: false
|
|
kkonganti@1
|
543
|
|
kkonganti@1
|
544 --fastp_cut_right : Move a sliding window from tail, drop the
|
|
kkonganti@1
|
545 bases in the window and the right part if
|
|
kkonganti@1
|
546 its mean quality < threshold, and then stop
|
|
kkonganti@1
|
547 . Default: true
|
|
kkonganti@1
|
548
|
|
kkonganti@1
|
549 --fastp_W : Sliding window size shared by --
|
|
kkonganti@1
|
550 fastp_cut_front, --fastp_cut_tail and --
|
|
kkonganti@1
|
551 fastp_cut_right. Default: 20
|
|
kkonganti@1
|
552
|
|
kkonganti@1
|
553 --fastp_M : The mean quality requirement shared by --
|
|
kkonganti@1
|
554 fastp_cut_front, --fastp_cut_tail and --
|
|
kkonganti@1
|
555 fastp_cut_right. Default: 30
|
|
kkonganti@1
|
556
|
|
kkonganti@1
|
557 --fastp_q : The quality value below which a base should
|
|
kkonganti@1
|
558 is not qualified. Default: 30
|
|
kkonganti@1
|
559
|
|
kkonganti@1
|
560 --fastp_u : What percent of bases are allowed to be
|
|
kkonganti@1
|
561 unqualified. Default: 40
|
|
kkonganti@1
|
562
|
|
kkonganti@1
|
563 --fastp_n : How many N's can a read have. Default: 5
|
|
kkonganti@1
|
564
|
|
kkonganti@1
|
565 --fastp_e : If the full reads' average quality is below
|
|
kkonganti@1
|
566 this value, then it is discarded. Default
|
|
kkonganti@1
|
567 : 0
|
|
kkonganti@1
|
568
|
|
kkonganti@1
|
569 --fastp_l : Reads shorter than this length will be
|
|
kkonganti@1
|
570 discarded. Default: 35
|
|
kkonganti@1
|
571
|
|
kkonganti@1
|
572 --fastp_max_len : Reads longer than this length will be
|
|
kkonganti@1
|
573 discarded. Default: 0
|
|
kkonganti@1
|
574
|
|
kkonganti@1
|
575 --fastp_y : Enable low complexity filter. The
|
|
kkonganti@1
|
576 complexity is defined as the percentage of
|
|
kkonganti@1
|
577 bases that are different from its next base
|
|
kkonganti@1
|
578 (base[i] != base[i+1]). Default: true
|
|
kkonganti@1
|
579
|
|
kkonganti@1
|
580 --fastp_Y : The threshold for low complexity filter (0~
|
|
kkonganti@1
|
581 100). Ex: A value of 30 means 30%
|
|
kkonganti@1
|
582 complexity is required. Default: 30
|
|
kkonganti@1
|
583
|
|
kkonganti@1
|
584 --fastp_U : Enable Unique Molecular Identifier (UMI)
|
|
kkonganti@1
|
585 pre-processing. Default: false
|
|
kkonganti@1
|
586
|
|
kkonganti@1
|
587 --fastp_umi_loc : Specify the location of UMI, can be one of
|
|
kkonganti@1
|
588 index1/index2/read1/read2/per_index/
|
|
kkonganti@1
|
589 per_read. Default: false
|
|
kkonganti@1
|
590
|
|
kkonganti@1
|
591 --fastp_umi_len : If the UMI is in read1 or read2, its length
|
|
kkonganti@1
|
592 should be provided. Default: false
|
|
kkonganti@1
|
593
|
|
kkonganti@1
|
594 --fastp_umi_prefix : If specified, an underline will be used to
|
|
kkonganti@1
|
595 connect prefix and UMI (i.e. prefix=UMI,
|
|
kkonganti@1
|
596 UMI=AATTCG, final=UMI_AATTCG). Default:
|
|
kkonganti@1
|
597 false
|
|
kkonganti@1
|
598
|
|
kkonganti@1
|
599 --fastp_umi_skip : If the UMI is in read1 or read2, fastp can
|
|
kkonganti@1
|
600 skip several bases following the UMI.
|
|
kkonganti@1
|
601 Default: false
|
|
kkonganti@1
|
602
|
|
kkonganti@1
|
603 --fastp_p : Enable overrepresented sequence analysis.
|
|
kkonganti@1
|
604 Default: true
|
|
kkonganti@1
|
605
|
|
kkonganti@1
|
606 --fastp_P : One in this many number of reads will be
|
|
kkonganti@1
|
607 computed for overrepresentation analysis (1
|
|
kkonganti@1
|
608 ~10000), smaller is slower. Default: 20
|
|
kkonganti@1
|
609
|
|
kkonganti@1
|
610 --fastp_use_custom_adapaters : Use custom adapter FASTA with fastp on top
|
|
kkonganti@1
|
611 of built-in adapter sequence auto-detection
|
|
kkonganti@1
|
612 . Enabling this option will attempt to find
|
|
kkonganti@1
|
613 and remove all possible Illumina adapter
|
|
kkonganti@1
|
614 and primer sequences but will make the
|
|
kkonganti@1
|
615 workflow run slow. Default: false
|
|
kkonganti@1
|
616
|
|
kkonganti@1
|
617 --mashscreen_run : Run `mash screen` tool. Default: true
|
|
kkonganti@1
|
618
|
|
kkonganti@1
|
619 --mashscreen_w : Winner-takes-all strategy for identity
|
|
kkonganti@1
|
620 estimates. After counting hashes for each
|
|
kkonganti@1
|
621 query, hashes that appear in multiple
|
|
kkonganti@1
|
622 queries will be removed from all except the
|
|
kkonganti@1
|
623 one with the best identity (ties broken by
|
|
kkonganti@1
|
624 larger query), and other identities will
|
|
kkonganti@1
|
625 be reduced. This removes output redundancy
|
|
kkonganti@1
|
626 , providing a rough compositional outline
|
|
kkonganti@1
|
627 . Default: false
|
|
kkonganti@1
|
628
|
|
kkonganti@1
|
629 --mashscreen_i : Minimum identity to report. Inclusive
|
|
kkonganti@1
|
630 unless set to zero, in which case only
|
|
kkonganti@1
|
631 identities greater than zero (i.e. with at
|
|
kkonganti@1
|
632 least one shared hash) will be reported.
|
|
kkonganti@1
|
633 Set to -1 to output everything. (-1-1).
|
|
kkonganti@1
|
634 Default: false
|
|
kkonganti@1
|
635
|
|
kkonganti@1
|
636 --mashscreen_v : Maximum p-value to report (0-1). Default:
|
|
kkonganti@1
|
637 false
|
|
kkonganti@1
|
638
|
|
kkonganti@1
|
639 --tuspy_run : Run the get_top_unique_mash_hits_genomes.py
|
|
kkonganti@1
|
640 script. Default: true
|
|
kkonganti@1
|
641
|
|
kkonganti@1
|
642 --tuspy_s : Absolute UNIX path to metadata text file
|
|
kkonganti@1
|
643 with the field separator, | and 5 fields:
|
|
kkonganti@1
|
644 serotype|asm_lvl|asm_url|snp_cluster_idEx:
|
|
kkonganti@1
|
645 serotype=Derby,antigen_formula=4:f,g:-|
|
|
kkonganti@1
|
646 Scaffold|402440|ftp://...|PDS000096654.2.
|
|
kkonganti@1
|
647 Mentioning this option will create a pickle
|
|
kkonganti@1
|
648 file for the provided metadata and exits.
|
|
kkonganti@1
|
649 Default: false
|
|
kkonganti@1
|
650
|
|
kkonganti@1
|
651 --tuspy_m : Absolute UNIX path to mash screen results
|
|
kkonganti@1
|
652 file. Default: false
|
|
kkonganti@1
|
653
|
|
kkonganti@1
|
654 --tuspy_ps : Absolute UNIX Path to serialized metadata
|
|
kkonganti@1
|
655 object in a pickle file. Default: /hpc/db/
|
|
kkonganti@1
|
656 bettercallsal/latest/index_metadata/
|
|
kkonganti@1
|
657 per_snp_cluster.ACC2SERO.pickle
|
|
kkonganti@1
|
658
|
|
kkonganti@1
|
659 --tuspy_gd : Absolute UNIX Path to directory containing
|
|
kkonganti@1
|
660 gzipped genome FASTA files. Default: /hpc/
|
|
kkonganti@1
|
661 db/bettercallsal/latest/scaffold_genomes
|
|
kkonganti@1
|
662
|
|
kkonganti@1
|
663 --tuspy_gds : Genome FASTA file suffix to search for in
|
|
kkonganti@1
|
664 the genome directory. Default:
|
|
kkonganti@1
|
665 _scaffolded_genomic.fna.gz
|
|
kkonganti@1
|
666
|
|
kkonganti@1
|
667 --tuspy_n : Return up to this many number of top N
|
|
kkonganti@1
|
668 unique genome accession hits. Default: 10
|
|
kkonganti@1
|
669
|
|
kkonganti@1
|
670 --sourmashsketch_run : Run `sourmash sketch dna` tool. Default:
|
|
kkonganti@1
|
671 true
|
|
kkonganti@1
|
672
|
|
kkonganti@1
|
673 --sourmashsketch_mode : Select which type of signatures to be
|
|
kkonganti@1
|
674 created: dna, protein, fromfile or
|
|
kkonganti@1
|
675 translate. Default: dna
|
|
kkonganti@1
|
676
|
|
kkonganti@1
|
677 --sourmashsketch_p : Signature parameters to use. Default: abund
|
|
kkonganti@1
|
678 ,scaled=1000,k=51,k=61,k=71
|
|
kkonganti@1
|
679
|
|
kkonganti@1
|
680 --sourmashsketch_file : <path> A text file containing a list of
|
|
kkonganti@1
|
681 sequence files to load. Default: false
|
|
kkonganti@1
|
682
|
|
kkonganti@1
|
683 --sourmashsketch_f : Recompute signatures even if the file
|
|
kkonganti@1
|
684 exists. Default: false
|
|
kkonganti@1
|
685
|
|
kkonganti@1
|
686 --sourmashsketch_merge : Merge all input files into one signature
|
|
kkonganti@1
|
687 file with the specified name. Default:
|
|
kkonganti@1
|
688 false
|
|
kkonganti@1
|
689
|
|
kkonganti@1
|
690 --sourmashsketch_singleton : Compute a signature for each sequence
|
|
kkonganti@1
|
691 record individually. Default: true
|
|
kkonganti@1
|
692
|
|
kkonganti@1
|
693 --sourmashsketch_name : Name the signature generated from each file
|
|
kkonganti@1
|
694 after the first record in the file.
|
|
kkonganti@1
|
695 Default: false
|
|
kkonganti@1
|
696
|
|
kkonganti@1
|
697 --sourmashsketch_randomize : Shuffle the list of input files randomly.
|
|
kkonganti@1
|
698 Default: false
|
|
kkonganti@1
|
699
|
|
kkonganti@1
|
700 --sourmashgather_run : Run `sourmash gather` tool. Default: true
|
|
kkonganti@1
|
701
|
|
kkonganti@1
|
702 --sourmashgather_n : Number of results to report. By default,
|
|
kkonganti@1
|
703 will terminate at --sourmashgather_thr_bp
|
|
kkonganti@1
|
704 value. Default: false
|
|
kkonganti@1
|
705
|
|
kkonganti@1
|
706 --sourmashgather_thr_bp : Reporting threshold (in bp) for estimated
|
|
kkonganti@1
|
707 overlap with remaining query. Default:
|
|
kkonganti@1
|
708 false
|
|
kkonganti@1
|
709
|
|
kkonganti@1
|
710 --sourmashgather_ignoreabn : Do NOT use k-mer abundances if present.
|
|
kkonganti@1
|
711 Default: false
|
|
kkonganti@1
|
712
|
|
kkonganti@1
|
713 --sourmashgather_prefetch : Use prefetch before gather. Default: false
|
|
kkonganti@1
|
714
|
|
kkonganti@1
|
715 --sourmashgather_noprefetch : Do not use prefetch before gather. Default
|
|
kkonganti@1
|
716 : false
|
|
kkonganti@1
|
717
|
|
kkonganti@1
|
718 --sourmashgather_ani_ci : Output confidence intervals for ANI
|
|
kkonganti@1
|
719 estimates. Default: true
|
|
kkonganti@1
|
720
|
|
kkonganti@1
|
721 --sourmashgather_k : The k-mer size to select. Default: 71
|
|
kkonganti@1
|
722
|
|
kkonganti@1
|
723 --sourmashgather_protein : Choose a protein signature. Default: false
|
|
kkonganti@1
|
724
|
|
kkonganti@1
|
725 --sourmashgather_noprotein : Do not choose a protein signature. Default
|
|
kkonganti@1
|
726 : false
|
|
kkonganti@1
|
727
|
|
kkonganti@1
|
728 --sourmashgather_dayhoff : Choose Dayhoff-encoded amino acid
|
|
kkonganti@1
|
729 signatures. Default: false
|
|
kkonganti@1
|
730
|
|
kkonganti@1
|
731 --sourmashgather_nodayhoff : Do not choose Dayhoff-encoded amino acid
|
|
kkonganti@1
|
732 signatures. Default: false
|
|
kkonganti@1
|
733
|
|
kkonganti@1
|
734 --sourmashgather_hp : Choose hydrophobic-polar-encoded amino acid
|
|
kkonganti@1
|
735 signatures. Default: false
|
|
kkonganti@1
|
736
|
|
kkonganti@1
|
737 --sourmashgather_nohp : Do not choose hydrophobic-polar-encoded
|
|
kkonganti@1
|
738 amino acid signatures. Default: false
|
|
kkonganti@1
|
739
|
|
kkonganti@1
|
740 --sourmashgather_dna : Choose DNA signature. Default: true
|
|
kkonganti@1
|
741
|
|
kkonganti@1
|
742 --sourmashgather_nodna : Do not choose DNA signature. Default: false
|
|
kkonganti@1
|
743
|
|
kkonganti@1
|
744 --sourmashgather_scaled : Scaled value should be between 100 and 1e6
|
|
kkonganti@1
|
745 . Default: false
|
|
kkonganti@1
|
746
|
|
kkonganti@1
|
747 --sourmashgather_inc_pat : Search only signatures that match this
|
|
kkonganti@1
|
748 pattern in name, filename, or md5. Default
|
|
kkonganti@1
|
749 : false
|
|
kkonganti@1
|
750
|
|
kkonganti@1
|
751 --sourmashgather_exc_pat : Search only signatures that do not match
|
|
kkonganti@1
|
752 this pattern in name, filename, or md5.
|
|
kkonganti@1
|
753 Default: false
|
|
kkonganti@1
|
754
|
|
kkonganti@1
|
755 --sourmashsearch_run : Run `sourmash search` tool. Default: false
|
|
kkonganti@1
|
756
|
|
kkonganti@1
|
757 --sourmashsearch_n : Number of results to report. By default,
|
|
kkonganti@1
|
758 will terminate at --sourmashsearch_thr
|
|
kkonganti@1
|
759 value. Default: false
|
|
kkonganti@1
|
760
|
|
kkonganti@1
|
761 --sourmashsearch_thr : Reporting threshold (similarity) to return
|
|
kkonganti@1
|
762 results. Default: 0
|
|
kkonganti@1
|
763
|
|
kkonganti@1
|
764 --sourmashsearch_contain : Score based on containment rather than
|
|
kkonganti@1
|
765 similarity. Default: false
|
|
kkonganti@1
|
766
|
|
kkonganti@1
|
767 --sourmashsearch_maxcontain : Score based on max containment rather than
|
|
kkonganti@1
|
768 similarity. Default: false
|
|
kkonganti@1
|
769
|
|
kkonganti@1
|
770 --sourmashsearch_ignoreabn : Do NOT use k-mer abundances if present.
|
|
kkonganti@1
|
771 Default: true
|
|
kkonganti@1
|
772
|
|
kkonganti@1
|
773 --sourmashsearch_ani_ci : Output confidence intervals for ANI
|
|
kkonganti@1
|
774 estimates. Default: false
|
|
kkonganti@1
|
775
|
|
kkonganti@1
|
776 --sourmashsearch_k : The k-mer size to select. Default: 71
|
|
kkonganti@1
|
777
|
|
kkonganti@1
|
778 --sourmashsearch_protein : Choose a protein signature. Default: false
|
|
kkonganti@1
|
779
|
|
kkonganti@1
|
780 --sourmashsearch_noprotein : Do not choose a protein signature. Default
|
|
kkonganti@1
|
781 : false
|
|
kkonganti@1
|
782
|
|
kkonganti@1
|
783 --sourmashsearch_dayhoff : Choose Dayhoff-encoded amino acid
|
|
kkonganti@1
|
784 signatures. Default: false
|
|
kkonganti@1
|
785
|
|
kkonganti@1
|
786 --sourmashsearch_nodayhoff : Do not choose Dayhoff-encoded amino acid
|
|
kkonganti@1
|
787 signatures. Default: false
|
|
kkonganti@1
|
788
|
|
kkonganti@1
|
789 --sourmashsearch_hp : Choose hydrophobic-polar-encoded amino acid
|
|
kkonganti@1
|
790 signatures. Default: false
|
|
kkonganti@1
|
791
|
|
kkonganti@1
|
792 --sourmashsearch_nohp : Do not choose hydrophobic-polar-encoded
|
|
kkonganti@1
|
793 amino acid signatures. Default: false
|
|
kkonganti@1
|
794
|
|
kkonganti@1
|
795 --sourmashsearch_dna : Choose DNA signature. Default: true
|
|
kkonganti@1
|
796
|
|
kkonganti@1
|
797 --sourmashsearch_nodna : Do not choose DNA signature. Default: false
|
|
kkonganti@1
|
798
|
|
kkonganti@1
|
799 --sourmashsearch_scaled : Scaled value should be between 100 and 1e6
|
|
kkonganti@1
|
800 . Default: false
|
|
kkonganti@1
|
801
|
|
kkonganti@1
|
802 --sourmashsearch_inc_pat : Search only signatures that match this
|
|
kkonganti@1
|
803 pattern in name, filename, or md5. Default
|
|
kkonganti@1
|
804 : false
|
|
kkonganti@1
|
805
|
|
kkonganti@1
|
806 --sourmashsearch_exc_pat : Search only signatures that do not match
|
|
kkonganti@1
|
807 this pattern in name, filename, or md5.
|
|
kkonganti@1
|
808 Default: false
|
|
kkonganti@1
|
809
|
|
kkonganti@1
|
810 --sfhpy_run : Run the sourmash_filter_hits.py script.
|
|
kkonganti@1
|
811 Default: true
|
|
kkonganti@1
|
812
|
|
kkonganti@1
|
813 --sfhpy_fcn : Column name by which filtering of rows
|
|
kkonganti@1
|
814 should be applied. Default: f_match
|
|
kkonganti@1
|
815
|
|
kkonganti@1
|
816 --sfhpy_fcv : Remove genomes whose match with the query
|
|
kkonganti@1
|
817 FASTQ is less than this much. Default: 0.1
|
|
kkonganti@1
|
818
|
|
kkonganti@1
|
819 --sfhpy_gt : Apply greather than or equal to condition
|
|
kkonganti@1
|
820 on numeric values of --sfhpy_fcn column.
|
|
kkonganti@1
|
821 Default: true
|
|
kkonganti@1
|
822
|
|
kkonganti@1
|
823 --sfhpy_lt : Apply less than or equal to condition on
|
|
kkonganti@1
|
824 numeric values of --sfhpy_fcn column.
|
|
kkonganti@1
|
825 Default: false
|
|
kkonganti@1
|
826
|
|
kkonganti@1
|
827 --kmaindex_run : Run kma index tool. Default: true
|
|
kkonganti@1
|
828
|
|
kkonganti@1
|
829 --kmaindex_t_db : Add to existing DB. Default: false
|
|
kkonganti@1
|
830
|
|
kkonganti@1
|
831 --kmaindex_k : k-mer size. Default: 31
|
|
kkonganti@1
|
832
|
|
kkonganti@1
|
833 --kmaindex_m : Minimizer size. Default: false
|
|
kkonganti@1
|
834
|
|
kkonganti@1
|
835 --kmaindex_hc : Homopolymer compression. Default: false
|
|
kkonganti@1
|
836
|
|
kkonganti@1
|
837 --kmaindex_ML : Minimum length of templates. Defaults to --
|
|
kkonganti@1
|
838 kmaindex_k Default: false
|
|
kkonganti@1
|
839
|
|
kkonganti@1
|
840 --kmaindex_ME : Mega DB. Default: false
|
|
kkonganti@1
|
841
|
|
kkonganti@1
|
842 --kmaindex_Sparse : Make Sparse DB. Default: false
|
|
kkonganti@1
|
843
|
|
kkonganti@1
|
844 --kmaindex_ht : Homology template. Default: false
|
|
kkonganti@1
|
845
|
|
kkonganti@1
|
846 --kmaindex_hq : Homology query. Default: false
|
|
kkonganti@1
|
847
|
|
kkonganti@1
|
848 --kmaindex_and : Both homology thresholds have to reach.
|
|
kkonganti@1
|
849 Default: false
|
|
kkonganti@1
|
850
|
|
kkonganti@1
|
851 --kmaindex_nbp : No bias print. Default: false
|
|
kkonganti@1
|
852
|
|
kkonganti@1
|
853 --kmaalign_run : Run kma tool. Default: true
|
|
kkonganti@1
|
854
|
|
kkonganti@1
|
855 --kmaalign_int : Input file has interleaved reads. Default
|
|
kkonganti@1
|
856 : false
|
|
kkonganti@1
|
857
|
|
kkonganti@1
|
858 --kmaalign_ef : Output additional features. Default: false
|
|
kkonganti@1
|
859
|
|
kkonganti@1
|
860 --kmaalign_vcf : Output vcf file. 2 to apply FT. Default:
|
|
kkonganti@1
|
861 false
|
|
kkonganti@1
|
862
|
|
kkonganti@1
|
863 --kmaalign_sam : Output SAM, 4/2096 for mapped/aligned.
|
|
kkonganti@1
|
864 Default: false
|
|
kkonganti@1
|
865
|
|
kkonganti@1
|
866 --kmaalign_nc : No consensus file. Default: true
|
|
kkonganti@1
|
867
|
|
kkonganti@1
|
868 --kmaalign_na : No aln file. Default: true
|
|
kkonganti@1
|
869
|
|
kkonganti@1
|
870 --kmaalign_nf : No frag file. Default: true
|
|
kkonganti@1
|
871
|
|
kkonganti@1
|
872 --kmaalign_a : Output all template mappings. Default:
|
|
kkonganti@1
|
873 false
|
|
kkonganti@1
|
874
|
|
kkonganti@1
|
875 --kmaalign_and : Use both -mrs and p-value on consensus.
|
|
kkonganti@1
|
876 Default: false
|
|
kkonganti@1
|
877
|
|
kkonganti@1
|
878 --kmaalign_oa : Use neither -mrs or p-value on consensus.
|
|
kkonganti@1
|
879 Default: false
|
|
kkonganti@1
|
880
|
|
kkonganti@1
|
881 --kmaalign_bc : Minimum support to call bases. Default:
|
|
kkonganti@1
|
882 false
|
|
kkonganti@1
|
883
|
|
kkonganti@1
|
884 --kmaalign_bcNano : Altered indel calling for ONT data. Default
|
|
kkonganti@1
|
885 : false
|
|
kkonganti@1
|
886
|
|
kkonganti@1
|
887 --kmaalign_bcd : Minimum depth to call bases. Default: false
|
|
kkonganti@1
|
888
|
|
kkonganti@1
|
889 --kmaalign_bcg : Maintain insignificant gaps. Default: false
|
|
kkonganti@1
|
890
|
|
kkonganti@1
|
891 --kmaalign_ID : Minimum consensus ID. Default: false
|
|
kkonganti@1
|
892
|
|
kkonganti@1
|
893 --kmaalign_md : Minimum depth. Default: false
|
|
kkonganti@1
|
894
|
|
kkonganti@1
|
895 --kmaalign_dense : Skip insertion in consensus. Default: false
|
|
kkonganti@1
|
896
|
|
kkonganti@1
|
897 --kmaalign_ref_fsa : Use Ns on indels. Default: false
|
|
kkonganti@1
|
898
|
|
kkonganti@1
|
899 --kmaalign_Mt1 : Map everything to one template. Default:
|
|
kkonganti@1
|
900 false
|
|
kkonganti@1
|
901
|
|
kkonganti@1
|
902 --kmaalign_1t1 : Map one query to one template. Default:
|
|
kkonganti@1
|
903 false
|
|
kkonganti@1
|
904
|
|
kkonganti@1
|
905 --kmaalign_mrs : Minimum relative alignment score. Default:
|
|
kkonganti@1
|
906 false
|
|
kkonganti@1
|
907
|
|
kkonganti@1
|
908 --kmaalign_mrc : Minimum query coverage. Default: 0.99
|
|
kkonganti@1
|
909
|
|
kkonganti@1
|
910 --kmaalign_mp : Minimum phred score of trailing and leading
|
|
kkonganti@1
|
911 bases. Default: 30
|
|
kkonganti@1
|
912
|
|
kkonganti@1
|
913 --kmaalign_mq : Set the minimum mapping quality. Default:
|
|
kkonganti@1
|
914 false
|
|
kkonganti@1
|
915
|
|
kkonganti@1
|
916 --kmaalign_eq : Minimum average quality score. Default: 30
|
|
kkonganti@1
|
917
|
|
kkonganti@1
|
918 --kmaalign_5p : Trim 5 prime by this many bases. Default:
|
|
kkonganti@1
|
919 false
|
|
kkonganti@1
|
920
|
|
kkonganti@1
|
921 --kmaalign_3p : Trim 3 prime by this many bases Default:
|
|
kkonganti@1
|
922 false
|
|
kkonganti@1
|
923
|
|
kkonganti@1
|
924 --kmaalign_apm : Sets both -pm and -fpm Default: false
|
|
kkonganti@1
|
925
|
|
kkonganti@1
|
926 --kmaalign_cge : Set CGE penalties and rewards Default:
|
|
kkonganti@1
|
927 false
|
|
kkonganti@1
|
928
|
|
kkonganti@1
|
929 --salmonidx_run : Run `salmon index` tool. Default: true
|
|
kkonganti@1
|
930
|
|
kkonganti@1
|
931 --salmonidx_k : The size of k-mers that should be used for
|
|
kkonganti@1
|
932 the quasi index. Default: false
|
|
kkonganti@1
|
933
|
|
kkonganti@1
|
934 --salmonidx_gencode : This flag will expect the input transcript
|
|
kkonganti@1
|
935 FASTA to be in GENCODE format, and will
|
|
kkonganti@1
|
936 split the transcript name at the first `|`
|
|
kkonganti@1
|
937 character. These reduced names will be used
|
|
kkonganti@1
|
938 in the output and when looking for these
|
|
kkonganti@1
|
939 transcripts in a gene to transcript GTF.
|
|
kkonganti@1
|
940 Default: false
|
|
kkonganti@1
|
941
|
|
kkonganti@1
|
942 --salmonidx_features : This flag will expect the input reference
|
|
kkonganti@1
|
943 to be in the tsv file format, and will
|
|
kkonganti@1
|
944 split the feature name at the first `tab`
|
|
kkonganti@1
|
945 character. These reduced names will be used
|
|
kkonganti@1
|
946 in the output and when looking for the
|
|
kkonganti@1
|
947 sequence of the features. GTF. Default:
|
|
kkonganti@1
|
948 false
|
|
kkonganti@1
|
949
|
|
kkonganti@1
|
950 --salmonidx_keepDuplicates : This flag will disable the default indexing
|
|
kkonganti@1
|
951 behavior of discarding sequence-identical
|
|
kkonganti@1
|
952 duplicate transcripts. If this flag is
|
|
kkonganti@1
|
953 passed then duplicate transcripts that
|
|
kkonganti@1
|
954 appear in the input will be retained and
|
|
kkonganti@1
|
955 quantified separately. Default: false
|
|
kkonganti@1
|
956
|
|
kkonganti@1
|
957 --salmonidx_keepFixedFasta : Retain the fixed fasta file (without short
|
|
kkonganti@1
|
958 transcripts and duplicates, clipped, etc.)
|
|
kkonganti@1
|
959 generated during indexing. Default: false
|
|
kkonganti@1
|
960
|
|
kkonganti@1
|
961 --salmonidx_filterSize : The size of the Bloom filter that will be
|
|
kkonganti@1
|
962 used by TwoPaCo during indexing. The filter
|
|
kkonganti@1
|
963 will be of size 2^{filterSize}. A value of
|
|
kkonganti@1
|
964 -1 means that the filter size will be
|
|
kkonganti@1
|
965 automatically set based on the number of
|
|
kkonganti@1
|
966 distinct k-mers in the input, as estimated
|
|
kkonganti@1
|
967 by nthll. Default: false
|
|
kkonganti@1
|
968
|
|
kkonganti@1
|
969 --salmonidx_sparse : Build the index using a sparse sampling of
|
|
kkonganti@1
|
970 k-mer positions This will require less
|
|
kkonganti@1
|
971 memory (especially during quantification),
|
|
kkonganti@1
|
972 but will take longer to constructand can
|
|
kkonganti@1
|
973 slow down mapping / alignment. Default:
|
|
kkonganti@1
|
974 false
|
|
kkonganti@1
|
975
|
|
kkonganti@1
|
976 --salmonidx_n : Do not clip poly-A tails from the ends of
|
|
kkonganti@1
|
977 target sequences. Default: false
|
|
kkonganti@1
|
978
|
|
kkonganti@1
|
979 --gsrpy_run : Run the gen_salmon_res_table.py script.
|
|
kkonganti@1
|
980 Default: true
|
|
kkonganti@1
|
981
|
|
kkonganti@1
|
982 --gsrpy_url : Generate an additional column in final
|
|
kkonganti@1
|
983 results table which links out to NCBI
|
|
kkonganti@1
|
984 Pathogens Isolate Browser. Default: true
|
|
kkonganti@1
|
985
|
|
kkonganti@1
|
986 Help options :
|
|
kkonganti@1
|
987
|
|
kkonganti@1
|
988 --help : Display this message.
|
|
kkonganti@1
|
989
|
|
kkonganti@1
|
990 ```
|
