Mercurial > repos > kkonganti > cfsan_bettercallsal
diff 0.5.0/readme/bettercallsal.md @ 1:365849f031fd
"planemo upload"
| author | kkonganti |
|---|---|
| date | Mon, 05 Jun 2023 18:48:51 -0400 |
| parents | |
| children |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/0.5.0/readme/bettercallsal.md Mon Jun 05 18:48:51 2023 -0400 @@ -0,0 +1,990 @@ +# bettercallsal + +`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. + +\ + + +<!-- TOC --> + +- [Minimum Requirements](#minimum-requirements) +- [Usage and Examples](#usage-and-examples) + - [Database](#database) + - [Input](#input) + - [Output](#output) + - [Computational resources](#computational-resources) + - [Runtime profiles](#runtime-profiles) + - [your_institution.config](#your_institutionconfig) + - [Cloud computing](#cloud-computing) + - [Example data](#example-data) +- [Using sourmash](#using-sourmash) +- [bettercallsal CLI Help](#bettercallsal-cli-help) + +<!-- /TOC --> + +\ + + +## Minimum Requirements + +1. [Nextflow version 22.10.0](https://github.com/nextflow-io/nextflow/releases/download/v22.10.0/nextflow). + - Make the `nextflow` binary executable (`chmod 755 nextflow`) and also make sure that it is made available in your `$PATH`. + - If your existing `JAVA` install does not support the newest **Nextflow** version, you can try **Amazon**'s `JAVA` (OpenJDK): [Corretto](https://corretto.aws/downloads/latest/amazon-corretto-17-x64-linux-jdk.tar.gz). +2. Either of `micromamba` or `docker` or `singularity` installed and made available in your `$PATH`. + - 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. + - 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 `$PATH`. + - Just the `curl` step is sufficient to download the binary as far as running the workflows are concerned. +3. Minimum of 10 CPU cores and about 16 GBs for main workflow steps. More memory may be required if your **FASTQ** files are big. + +\ + + +## Usage and Examples + +Clone or download this repository and then call `cpipes`. + +```bash +cpipes --pipeline bettercallsal [options] +``` + +\ + + +**Example**: Run the default `bettercallsal` pipeline in single-end mode. + +```bash +cd /data/scratch/$USER +mkdir nf-cpipes +cd nf-cpipes +cpipes + --pipeline bettercallsal \ + --input /path/to/illumina/fastq/dir \ + --output /path/to/output \ + --bcs_root_dbdir /data/Kranti_Konganti/bettercallsal_db +``` + +\ + + +**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`. + +```bash +cd /data/scratch/$USER +mkdir nf-cpipes +cd nf-cpipes +cpipes \ + --pipeline bettercallsal \ + --input /path/to/illumina/fastq/dir \ + --output /path/to/output \ + --bcs_root_dbdir /data/Kranti_Konganti/bettercallsal_db \ + --fq_single_end false \ + --fq_suffix '_R1_001.fastq.gz' +``` + +\ + + +### Database + +--- + +The successful run of the workflow requires certain database flat files specific for the workflow. + +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. + + + +### Input + +--- + +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. + +For example, if the directory contains FASTQ files as shown below: + +- KB-01_apple_L001_R1.fastq.gz +- KB-01_apple_L001_R2.fastq.gz +- KB-01_apple_L002_R1.fastq.gz +- KB-01_apple_L002_R2.fastq.gz +- KB-02_mango_L001_R1.fastq.gz +- KB-02_mango_L001_R2.fastq.gz +- KB-02_mango_L002_R1.fastq.gz +- KB-02_mango_L002_R2.fastq.gz + +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`). + +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. + +\ + + +### Output + +--- + +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. + +\ + + +### Computational resources + +--- + +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. + +\ + + +Example: + +```bash +cpipes \ + --pipeline bettercallsal \ + --input /path/to/bettercallsal_sim_reads \ + --output /path/to/bettercallsal_sim_reads_output \ + --bcs_root_dbdir /path/to/PDG000000002.2537 + --kmaalign_ignorequals \ + --max_cpus 5 \ + -profile stdkondagac \ + -resume +``` + +\ + + +### Runtime profiles + +--- + +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. + +\ + + +Example: + +```bash +cd /data/scratch/$USER +mkdir nf-cpipes +cd nf-cpipes +cpipes \ + --pipeline bettercallsal \ + --input /path/to/fastq_pass_dir \ + --output /path/to/where/output/should/go \ + -profile your_institution +``` + +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. + +\ + + +### `your_institution.config` + +--- + +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: + +\ + + +```groovy +your_institution { + process.executor = 'sge' + process.queue = 'normal.q' + singularity.enabled = false + singularity.autoMounts = true + docker.enabled = false + params.enable_conda = true + conda.enabled = true + conda.useMicromamba = true + params.enable_module = false +} +``` + +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. + +\ + + +### Cloud computing + +--- + +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): + +\ + + +Example: + +```groovy +my_aws_batch { + executor = 'awsbatch' + queue = 'my-batch-queue' + aws.batch.cliPath = '/home/ec2-user/miniconda/bin/aws' + aws.batch.region = 'us-east-1' + singularity.enabled = false + singularity.autoMounts = true + docker.enabled = true + params.conda_enabled = false + params.enable_module = false +} +``` + +\ + + +### Example data + +--- + +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. + +- Download simulated reads: [S3](https://cfsan-pub-xfer.s3.amazonaws.com/Kranti.Konganti/bettercallsal/bettercallsal_sim_reads.tar.bz2) (~ 3 GB). +- 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. +- 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). +- 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). + +Now run the workflow by ignoring quality values since these are simulated base qualities: + +\ + + +```bash +cpipes \ + --pipeline bettercallsal \ + --input /path/to/bettercallsal_sim_reads \ + --output /path/to/bettercallsal_sim_reads_output \ + --bcs_root_dbdir /path/to/PDG000000002.2537 + --kmaalign_ignorequals \ + -profile stdkondagac \ + -resume +``` + +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. + +\ + + +## Using `sourmash` + +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. + +You can turn **OFF** this feature with `--sourmashsketch_run false` option. + +\ + + +## `bettercallsal` CLI Help + +```text +[Kranti_Konganti@my-unix-box ]$ cpipes --pipeline bettercallsal --help +N E X T F L O W ~ version 22.10.0 +Launching `./bettercallsal/cpipes` [awesome_chandrasekhar] DSL2 - revision: 8da4e11078 +================================================================================ + (o) + ___ _ __ _ _ __ ___ ___ + / __|| '_ \ | || '_ \ / _ \/ __| +| (__ | |_) || || |_) || __/\__ \ + \___|| .__/ |_|| .__/ \___||___/ + | | | | + |_| |_| +-------------------------------------------------------------------------------- +A collection of modular pipelines at CFSAN, FDA. +-------------------------------------------------------------------------------- +Name : CPIPES +Author : Kranti Konganti +Version : 0.5.0 +Center : CFSAN, FDA. +================================================================================ + +Workflow : bettercallsal + +Author : Kranti Konganti + +Version : 0.5.0 + + +Usage : cpipes --pipeline bettercallsal [options] + + +Required : + +--input : Absolute path to directory containing FASTQ + files. The directory should contain only + FASTQ files as all the files within the + mentioned directory will be read. Ex: -- + input /path/to/fastq_pass + +--output : Absolute path to directory where all the + pipeline outputs should be stored. Ex: -- + output /path/to/output + +Other options : + +--metadata : Absolute path to metadata CSV file + containing five mandatory columns: sample, + fq1,fq2,strandedness,single_end. The fq1 + and fq2 columns contain absolute paths to + the FASTQ files. This option can be used in + place of --input option. This is rare. Ex + : --metadata samplesheet.csv + +--fq_suffix : The suffix of FASTQ files (Unpaired reads + or R1 reads or Long reads) if an input + directory is mentioned via --input option. + Default: .fastq.gz + +--fq2_suffix : The suffix of FASTQ files (Paired-end reads + or R2 reads) if an input directory is + mentioned via --input option. Default: + _R2_001.fastq.gz + +--fq_filter_by_len : Remove FASTQ reads that are less than this + many bases. Default: 0 + +--fq_strandedness : The strandedness of the sequencing run. + This is mostly needed if your sequencing + run is RNA-SEQ. For most of the other runs + , it is probably safe to use unstranded for + the option. Default: unstranded + +--fq_single_end : SINGLE-END information will be auto- + detected but this option forces PAIRED-END + FASTQ files to be treated as SINGLE-END so + only read 1 information is included in auto + -generated samplesheet. Default: true + +--fq_filename_delim : Delimiter by which the file name is split + to obtain sample name. Default: _ + +--fq_filename_delim_idx : After splitting FASTQ file name by using + the --fq_filename_delim option, all + elements before this index (1-based) will + be joined to create final sample name. + Default: 1 + +--bcs_concat_pe : Concatenate paired-end files. Default: true + +--bbmerge_run : Run BBMerge tool. Default: false + +--bbmerge_reads : Quit after this many read pairs (-1 means + all) Default: -1 + +--bbmerge_adapters : Absolute UNIX path pointing to the adapters + file in FASTA format. Default: false + +--bbmerge_ziplevel : Set to 1 (lowest) through 9 (max) to change + compression level; lower compression is + faster. Default: 1 + +--bbmerge_ordered : Output reads in the same order as input. + Default: false + +--bbmerge_qtrim : Trim read ends to remove bases with quality + below --bbmerge_minq. Trims BEFORE merging + . Values: t (trim both ends), f (neither + end), r (right end only), l (left end only + ). Default: true + +--bbmerge_qtrim2 : May be specified instead of --bbmerge_qtrim + to perform trimming only if merging is + unsuccesful. then retry merging. Default: + false + +--bbmerge_trimq : Trim quality threshold. This may be comma- + delimited list (ascending) to try multiple + values. Default: 10 + +--bbmerge_minlength : (ml) Reads shorter than this after trimming + , but before merging, will be discarded. + Pairs will be discarded onlyif both are + shorter. Default: 1 + +--bbmerge_tbo : (trimbyoverlap). Trim overlapping reads to + remove right most (3') non-overlaping + portion instead of joining Default: false + +--bbmerge_minavgquality : (maq). Reads with average quality below + this after trimming will not be attempted + to merge. Default: 30 + +--bbmerge_trimpolya : Trim trailing poly-A tail from adapter + output. Only affects outadapter. This also + trims poly-A followed by poly-G, which + occurs on NextSeq. Default: true + +--bbmerge_pfilter : Ban improbable overlaps. Higher is more + strict. 0 will disable the filter; 1 will + allow only perfect overlaps. Default: 1 + +--bbmerge_ouq : Calculate best overlap using quality values + . Default: false + +--bbmerge_owq : Calculate best overlap without using + quality values. Default: true + +--bbmerge_strict : Decrease false positive rate and merging + rate. Default: false + +--bbmerge_verystrict : Greatly decrease false positive rate and + merging rate. Default: false + +--bbmerge_ultrastrict : Decrease false positive rate and merging + rate even more. Default: true + +--bbmerge_maxstrict : Maxiamally decrease false positive rate and + merging rate. Default: false + +--bbmerge_loose : Increase false positive rate and merging + rate. Default: false + +--bbmerge_veryloose : Greatly increase false positive rate and + merging rate. Default: false + +--bbmerge_ultraloose : Increase false positive rate and merging + rate even more. Default: false + +--bbmerge_maxloose : Maximally increase false positive rate and + merging rate. Default: false + +--bbmerge_fast : Fastest possible preset. Default: false + +--bbmerge_k : Kmer length. 31 (or less) is fastest and + uses the least memory, but higher values + may be more accurate. 60 tends to work well + for 150bp reads. Default: 60 + +--bbmerge_prealloc : Pre-allocate memory rather than dynamically + growing. Faster and more memory-efficient + for large datasets. A float fraction (0-1) + may be specified, default 1. Default: true + +--fastp_run : Run fastp tool. Default: true + +--fastp_failed_out : Specify whether to store reads that cannot + pass the filters. Default: false + +--fastp_merged_out : Specify whether to store merged output or + not. Default: false + +--fastp_overlapped_out : For each read pair, output the overlapped + region if it has no mismatched base. + Default: false + +--fastp_6 : Indicate that the input is using phred64 + scoring (it'll be converted to phred33, so + the output will still be phred33). Default + : false + +--fastp_reads_to_process : Specify how many reads/pairs are to be + processed. Default value 0 means process + all reads. Default: 0 + +--fastp_fix_mgi_id : The MGI FASTQ ID format is not compatible + with many BAM operation tools, enable this + option to fix it. Default: false + +--fastp_A : Disable adapter trimming. On by default. + Default: false + +--fastp_adapter_fasta : Specify a FASTA file to trim both read1 and + read2 (if PE) by all the sequences in this + FASTA file. Default: false + +--fastp_f : Trim how many bases in front of read1. + Default: 0 + +--fastp_t : Trim how many bases at the end of read1. + Default: 0 + +--fastp_b : Max length of read1 after trimming. Default + : 0 + +--fastp_F : Trim how many bases in front of read2. + Default: 0 + +--fastp_T : Trim how many bases at the end of read2. + Default: 0 + +--fastp_B : Max length of read2 after trimming. Default + : 0 + +--fastp_dedup : Enable deduplication to drop the duplicated + reads/pairs. Default: true + +--fastp_dup_calc_accuracy : Accuracy level to calculate duplication (1~ + 6), higher level uses more memory (1G, 2G, + 4G, 8G, 16G, 24G). Default 1 for no-dedup + mode, and 3 for dedup mode. Default: 6 + +--fastp_poly_g_min_len : The minimum length to detect polyG in the + read tail. Default: 10 + +--fastp_G : Disable polyG tail trimming. Default: true + +--fastp_x : Enable polyX trimming in 3' ends. Default: + false + +--fastp_poly_x_min_len : The minimum length to detect polyX in the + read tail. Default: 10 + +--fastp_cut_front : Move a sliding window from front (5') to + tail, drop the bases in the window if its + mean quality < threshold, stop otherwise. + Default: true + +--fastp_cut_tail : Move a sliding window from tail (3') to + front, drop the bases in the window if its + mean quality < threshold, stop otherwise. + Default: false + +--fastp_cut_right : Move a sliding window from tail, drop the + bases in the window and the right part if + its mean quality < threshold, and then stop + . Default: true + +--fastp_W : Sliding window size shared by -- + fastp_cut_front, --fastp_cut_tail and -- + fastp_cut_right. Default: 20 + +--fastp_M : The mean quality requirement shared by -- + fastp_cut_front, --fastp_cut_tail and -- + fastp_cut_right. Default: 30 + +--fastp_q : The quality value below which a base should + is not qualified. Default: 30 + +--fastp_u : What percent of bases are allowed to be + unqualified. Default: 40 + +--fastp_n : How many N's can a read have. Default: 5 + +--fastp_e : If the full reads' average quality is below + this value, then it is discarded. Default + : 0 + +--fastp_l : Reads shorter than this length will be + discarded. Default: 35 + +--fastp_max_len : Reads longer than this length will be + discarded. Default: 0 + +--fastp_y : Enable low complexity filter. The + complexity is defined as the percentage of + bases that are different from its next base + (base[i] != base[i+1]). Default: true + +--fastp_Y : The threshold for low complexity filter (0~ + 100). Ex: A value of 30 means 30% + complexity is required. Default: 30 + +--fastp_U : Enable Unique Molecular Identifier (UMI) + pre-processing. Default: false + +--fastp_umi_loc : Specify the location of UMI, can be one of + index1/index2/read1/read2/per_index/ + per_read. Default: false + +--fastp_umi_len : If the UMI is in read1 or read2, its length + should be provided. Default: false + +--fastp_umi_prefix : If specified, an underline will be used to + connect prefix and UMI (i.e. prefix=UMI, + UMI=AATTCG, final=UMI_AATTCG). Default: + false + +--fastp_umi_skip : If the UMI is in read1 or read2, fastp can + skip several bases following the UMI. + Default: false + +--fastp_p : Enable overrepresented sequence analysis. + Default: true + +--fastp_P : One in this many number of reads will be + computed for overrepresentation analysis (1 + ~10000), smaller is slower. Default: 20 + +--fastp_use_custom_adapaters : Use custom adapter FASTA with fastp on top + of built-in adapter sequence auto-detection + . Enabling this option will attempt to find + and remove all possible Illumina adapter + and primer sequences but will make the + workflow run slow. Default: false + +--mashscreen_run : Run `mash screen` tool. Default: true + +--mashscreen_w : Winner-takes-all strategy for identity + estimates. After counting hashes for each + query, hashes that appear in multiple + queries will be removed from all except the + one with the best identity (ties broken by + larger query), and other identities will + be reduced. This removes output redundancy + , providing a rough compositional outline + . Default: false + +--mashscreen_i : Minimum identity to report. Inclusive + unless set to zero, in which case only + identities greater than zero (i.e. with at + least one shared hash) will be reported. + Set to -1 to output everything. (-1-1). + Default: false + +--mashscreen_v : Maximum p-value to report (0-1). Default: + false + +--tuspy_run : Run the get_top_unique_mash_hits_genomes.py + script. Default: true + +--tuspy_s : Absolute UNIX path to metadata text file + with the field separator, | and 5 fields: + serotype|asm_lvl|asm_url|snp_cluster_idEx: + serotype=Derby,antigen_formula=4:f,g:-| + Scaffold|402440|ftp://...|PDS000096654.2. + Mentioning this option will create a pickle + file for the provided metadata and exits. + Default: false + +--tuspy_m : Absolute UNIX path to mash screen results + file. Default: false + +--tuspy_ps : Absolute UNIX Path to serialized metadata + object in a pickle file. Default: /hpc/db/ + bettercallsal/latest/index_metadata/ + per_snp_cluster.ACC2SERO.pickle + +--tuspy_gd : Absolute UNIX Path to directory containing + gzipped genome FASTA files. Default: /hpc/ + db/bettercallsal/latest/scaffold_genomes + +--tuspy_gds : Genome FASTA file suffix to search for in + the genome directory. Default: + _scaffolded_genomic.fna.gz + +--tuspy_n : Return up to this many number of top N + unique genome accession hits. Default: 10 + +--sourmashsketch_run : Run `sourmash sketch dna` tool. Default: + true + +--sourmashsketch_mode : Select which type of signatures to be + created: dna, protein, fromfile or + translate. Default: dna + +--sourmashsketch_p : Signature parameters to use. Default: abund + ,scaled=1000,k=51,k=61,k=71 + +--sourmashsketch_file : <path> A text file containing a list of + sequence files to load. Default: false + +--sourmashsketch_f : Recompute signatures even if the file + exists. Default: false + +--sourmashsketch_merge : Merge all input files into one signature + file with the specified name. Default: + false + +--sourmashsketch_singleton : Compute a signature for each sequence + record individually. Default: true + +--sourmashsketch_name : Name the signature generated from each file + after the first record in the file. + Default: false + +--sourmashsketch_randomize : Shuffle the list of input files randomly. + Default: false + +--sourmashgather_run : Run `sourmash gather` tool. Default: true + +--sourmashgather_n : Number of results to report. By default, + will terminate at --sourmashgather_thr_bp + value. Default: false + +--sourmashgather_thr_bp : Reporting threshold (in bp) for estimated + overlap with remaining query. Default: + false + +--sourmashgather_ignoreabn : Do NOT use k-mer abundances if present. + Default: false + +--sourmashgather_prefetch : Use prefetch before gather. Default: false + +--sourmashgather_noprefetch : Do not use prefetch before gather. Default + : false + +--sourmashgather_ani_ci : Output confidence intervals for ANI + estimates. Default: true + +--sourmashgather_k : The k-mer size to select. Default: 71 + +--sourmashgather_protein : Choose a protein signature. Default: false + +--sourmashgather_noprotein : Do not choose a protein signature. Default + : false + +--sourmashgather_dayhoff : Choose Dayhoff-encoded amino acid + signatures. Default: false + +--sourmashgather_nodayhoff : Do not choose Dayhoff-encoded amino acid + signatures. Default: false + +--sourmashgather_hp : Choose hydrophobic-polar-encoded amino acid + signatures. Default: false + +--sourmashgather_nohp : Do not choose hydrophobic-polar-encoded + amino acid signatures. Default: false + +--sourmashgather_dna : Choose DNA signature. Default: true + +--sourmashgather_nodna : Do not choose DNA signature. Default: false + +--sourmashgather_scaled : Scaled value should be between 100 and 1e6 + . Default: false + +--sourmashgather_inc_pat : Search only signatures that match this + pattern in name, filename, or md5. Default + : false + +--sourmashgather_exc_pat : Search only signatures that do not match + this pattern in name, filename, or md5. + Default: false + +--sourmashsearch_run : Run `sourmash search` tool. Default: false + +--sourmashsearch_n : Number of results to report. By default, + will terminate at --sourmashsearch_thr + value. Default: false + +--sourmashsearch_thr : Reporting threshold (similarity) to return + results. Default: 0 + +--sourmashsearch_contain : Score based on containment rather than + similarity. Default: false + +--sourmashsearch_maxcontain : Score based on max containment rather than + similarity. Default: false + +--sourmashsearch_ignoreabn : Do NOT use k-mer abundances if present. + Default: true + +--sourmashsearch_ani_ci : Output confidence intervals for ANI + estimates. Default: false + +--sourmashsearch_k : The k-mer size to select. Default: 71 + +--sourmashsearch_protein : Choose a protein signature. Default: false + +--sourmashsearch_noprotein : Do not choose a protein signature. Default + : false + +--sourmashsearch_dayhoff : Choose Dayhoff-encoded amino acid + signatures. Default: false + +--sourmashsearch_nodayhoff : Do not choose Dayhoff-encoded amino acid + signatures. Default: false + +--sourmashsearch_hp : Choose hydrophobic-polar-encoded amino acid + signatures. Default: false + +--sourmashsearch_nohp : Do not choose hydrophobic-polar-encoded + amino acid signatures. Default: false + +--sourmashsearch_dna : Choose DNA signature. Default: true + +--sourmashsearch_nodna : Do not choose DNA signature. Default: false + +--sourmashsearch_scaled : Scaled value should be between 100 and 1e6 + . Default: false + +--sourmashsearch_inc_pat : Search only signatures that match this + pattern in name, filename, or md5. Default + : false + +--sourmashsearch_exc_pat : Search only signatures that do not match + this pattern in name, filename, or md5. + Default: false + +--sfhpy_run : Run the sourmash_filter_hits.py script. + Default: true + +--sfhpy_fcn : Column name by which filtering of rows + should be applied. Default: f_match + +--sfhpy_fcv : Remove genomes whose match with the query + FASTQ is less than this much. Default: 0.1 + +--sfhpy_gt : Apply greather than or equal to condition + on numeric values of --sfhpy_fcn column. + Default: true + +--sfhpy_lt : Apply less than or equal to condition on + numeric values of --sfhpy_fcn column. + Default: false + +--kmaindex_run : Run kma index tool. Default: true + +--kmaindex_t_db : Add to existing DB. Default: false + +--kmaindex_k : k-mer size. Default: 31 + +--kmaindex_m : Minimizer size. Default: false + +--kmaindex_hc : Homopolymer compression. Default: false + +--kmaindex_ML : Minimum length of templates. Defaults to -- + kmaindex_k Default: false + +--kmaindex_ME : Mega DB. Default: false + +--kmaindex_Sparse : Make Sparse DB. Default: false + +--kmaindex_ht : Homology template. Default: false + +--kmaindex_hq : Homology query. Default: false + +--kmaindex_and : Both homology thresholds have to reach. + Default: false + +--kmaindex_nbp : No bias print. Default: false + +--kmaalign_run : Run kma tool. Default: true + +--kmaalign_int : Input file has interleaved reads. Default + : false + +--kmaalign_ef : Output additional features. Default: false + +--kmaalign_vcf : Output vcf file. 2 to apply FT. Default: + false + +--kmaalign_sam : Output SAM, 4/2096 for mapped/aligned. + Default: false + +--kmaalign_nc : No consensus file. Default: true + +--kmaalign_na : No aln file. Default: true + +--kmaalign_nf : No frag file. Default: true + +--kmaalign_a : Output all template mappings. Default: + false + +--kmaalign_and : Use both -mrs and p-value on consensus. + Default: false + +--kmaalign_oa : Use neither -mrs or p-value on consensus. + Default: false + +--kmaalign_bc : Minimum support to call bases. Default: + false + +--kmaalign_bcNano : Altered indel calling for ONT data. Default + : false + +--kmaalign_bcd : Minimum depth to call bases. Default: false + +--kmaalign_bcg : Maintain insignificant gaps. Default: false + +--kmaalign_ID : Minimum consensus ID. Default: false + +--kmaalign_md : Minimum depth. Default: false + +--kmaalign_dense : Skip insertion in consensus. Default: false + +--kmaalign_ref_fsa : Use Ns on indels. Default: false + +--kmaalign_Mt1 : Map everything to one template. Default: + false + +--kmaalign_1t1 : Map one query to one template. Default: + false + +--kmaalign_mrs : Minimum relative alignment score. Default: + false + +--kmaalign_mrc : Minimum query coverage. Default: 0.99 + +--kmaalign_mp : Minimum phred score of trailing and leading + bases. Default: 30 + +--kmaalign_mq : Set the minimum mapping quality. Default: + false + +--kmaalign_eq : Minimum average quality score. Default: 30 + +--kmaalign_5p : Trim 5 prime by this many bases. Default: + false + +--kmaalign_3p : Trim 3 prime by this many bases Default: + false + +--kmaalign_apm : Sets both -pm and -fpm Default: false + +--kmaalign_cge : Set CGE penalties and rewards Default: + false + +--salmonidx_run : Run `salmon index` tool. Default: true + +--salmonidx_k : The size of k-mers that should be used for + the quasi index. Default: false + +--salmonidx_gencode : This flag will expect the input transcript + FASTA to be in GENCODE format, and will + split the transcript name at the first `|` + character. These reduced names will be used + in the output and when looking for these + transcripts in a gene to transcript GTF. + Default: false + +--salmonidx_features : This flag will expect the input reference + to be in the tsv file format, and will + split the feature name at the first `tab` + character. These reduced names will be used + in the output and when looking for the + sequence of the features. GTF. Default: + false + +--salmonidx_keepDuplicates : This flag will disable the default indexing + behavior of discarding sequence-identical + duplicate transcripts. If this flag is + passed then duplicate transcripts that + appear in the input will be retained and + quantified separately. Default: false + +--salmonidx_keepFixedFasta : Retain the fixed fasta file (without short + transcripts and duplicates, clipped, etc.) + generated during indexing. Default: false + +--salmonidx_filterSize : The size of the Bloom filter that will be + used by TwoPaCo during indexing. The filter + will be of size 2^{filterSize}. A value of + -1 means that the filter size will be + automatically set based on the number of + distinct k-mers in the input, as estimated + by nthll. Default: false + +--salmonidx_sparse : Build the index using a sparse sampling of + k-mer positions This will require less + memory (especially during quantification), + but will take longer to constructand can + slow down mapping / alignment. Default: + false + +--salmonidx_n : Do not clip poly-A tails from the ends of + target sequences. Default: false + +--gsrpy_run : Run the gen_salmon_res_table.py script. + Default: true + +--gsrpy_url : Generate an additional column in final + results table which links out to NCBI + Pathogens Isolate Browser. Default: true + +Help options : + +--help : Display this message. + +```