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date Fri, 15 May 2026 17:50:45 +0000
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1 # SeqSero2S
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2
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3 Salmonella serotype prediction from genome sequencing data.
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4
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5 Online version: http://www.denglab.info/SeqSero2
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6
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7 # Updates since SS2 v1.2.1
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8 1. Convert the sequences of the following alleles to their reverse complement sequences in the SeqSero2 database.
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9 ```
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10 -fliC_b_Wien_CDC_b,d,j__1488\
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11 -fliC_d_from-II-48:d:z6_SRR1168371__1521\
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12 -fliC_a_Salmonella.enterica_from-cdc-Stk2184_other.a__1488
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13 -fliC_l,v_from-Nchanga_SRR1153349__1503
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14 -fliC_l,z13,z28_Salmonella.enterica_from-CDC_2011K-0215_l,v__1506
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15 -fljB_1,7_Salmonella.enterica_from-cdc_Stk1415_1__1521
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16 -fljB_1,5_from-cdc_Stk2184_1__1521
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17 -fljB_1,5_from-Infantis-micro-assembly_SRR1106258_1__1521
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18 -fljB_z6_from-II-48:d:z6_SRR1168371__1503
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19 ```
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20 2. Delete the following alleles from the SeqSero2 database because of the existence of mutations.
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21 ```
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22 -fliC_y_Bareillystr_AOZP01000027_other.y__1508
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23 -fliC_d_Muenchenstr_ARYW01000085_b,d,j__1496
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24 -fliC_d_Muenchenstr_ARYX01000110_b,d,j__1488
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25 -fliC_g,m_Enteritidisstr_ALHD01000038_g,m__1507
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26 -fljB_1,2_Newportstr_AYDZ01000021_1__1510
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27 ```
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28 2. Add a fliC 1,5,7 allele and a fliC 1,2,7 allele into the SeqSero2 database.
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29 ```
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30 -fliC_1,5,7_Salmonella.enterica_from-cdc-Stk1778_1,5,7_1521
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31 -fliC_1,2,7_Salmonella.enterica_from-cdc-Stk2293_1,2,7_1521
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32 ```
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33 3. Delete the O54 allele
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34 ```
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35 -O-54_wbbF__1380
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36 ```
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37 4. Fixed the bug that caused the misidentification of O9 and O2 by the micro-assembly workflow
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38 5. Update serotype names based on the simplified KWS scheme
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39 6. Remove the 9,46,27 allele
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40 ```
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41 -O-9,46,27_partial_wzy__1019
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42 ```
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43 7. Remove two fljB_1,2 allels
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44 ```
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45 -fljB_1,2_from-Brazzaville_SRR2058145_1__1521
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46 -fljB_1,2_Salmonella.enterica_1,4,5,12:i:1,2,7_AY353272_1__1521
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47 ```
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48 8. Run 7-gene MLST analysis using stringMLST/mlst
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49
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50 # Introduction
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51 SeqSero2S is a pipeline for Salmonella serotype prediction from raw sequencing reads or genome assemblies
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52
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53 # Dependencies
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54 SeqSero2S has three workflows:
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55
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56 (A) Allele micro-assembly (default). This workflow takes raw reads as input and performs targeted assembly of serotype determinant alleles. Assembled alleles are used to predict serotype and flag potential inter-serotype contamination in sequencing data (i.e., presence of reads from multiple serotypes due to, for example, cross or carryover contamination during sequencing).
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57
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58 Allele micro-assembly workflow depends on:
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59
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60 1. Python 3;
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61 2. Biopython 1.73;
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62 3. [Burrows-Wheeler Aligner v0.7.12](http://sourceforge.net/projects/bio-bwa/files/);
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63 4. [Samtools v1.8](http://sourceforge.net/projects/samtools/files/samtools/);
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64 5. [NCBI BLAST v2.2.28+](https://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE_TYPE=BlastDocs&DOC_TYPE=Download);
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65 6. [SRA Toolkit v2.8.0](http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd=show&f=software&m=software&s=software);
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66 7. [SPAdes v3.9.0](http://bioinf.spbau.ru/spades);
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67 8. [Bedtools v2.17.0](http://bedtools.readthedocs.io/en/latest/);
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68 9. [SalmID v0.11](https://github.com/hcdenbakker/SalmID);
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69 10. [stringMLST v0.6.3](https://github.com/jordanlab/stringMLST);
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70
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71 (B) Raw reads k-mer. This workflow takes raw reads as input and performs rapid serotype prediction based on unique k-mers of serotype determinants.
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72
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73 Raw reads k-mer workflow (originally SeqSeroK) depends on:
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74
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75 1. Python 3;
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76 2. [SRA Toolkit](http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd=show&f=software&m=software&s=software) (optional, just used to fastq-dump sra files);
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77 3. [mlst v2.22.1](https://github.com/tseemann/mlst).
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78
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79
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80 (C) Genome assembly k-mer. This workflow takes genome assemblies as input and the rest of the workflow largely overlaps with the raw reads k-mer workflow
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81
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82 # Installation
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83 ### Git
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84 Install mlst and stringMLST first
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85 ```
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86 conda install mlst
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87 ```
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88 ```
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89 pip install stringMLST
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90 ```
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91 To install the SeqSero2S git repository locally:
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92 ```
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93 git clone https://github.com/LSTUGA/SeqSero2S.git
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94 cd SeqSero2S
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95 python3 -m pip install --user .
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96 ```
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97
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98 # Executing the code
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99 Make sure all SeqSero2S and its dependency executables are added to your path (e.g. to ~/.bashrc). Then type SeqSero2S.py to get detailed instructions.
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100
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101 Usage: SeqSero2S.py
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102
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103 -m <string> (which workflow to apply, 'a'(raw reads allele micro-assembly), 'k'(raw reads and genome assembly k-mer), default=a)
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104
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105 -t <string> (input data type, '1' for interleaved paired-end reads, '2' for separated paired-end reads, '3' for single reads, '4' for genome assembly, '5' for nanopore reads (fasta/fastq))
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106
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107 -i <file> (/path/to/input/file)
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108
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109 -p <int> (number of threads for allele mode, if p >4, only 4 threads will be used for assembly since the amount of extracted reads is small, default=1)
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110
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111 -b <string> (algorithms for bwa mapping for allele mode; 'mem' for mem, 'sam' for samse/sampe; default=mem; optional; for now we only optimized for default "mem" mode)
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112
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113 -d <string> (output directory name, if not set, the output directory would be 'SeqSero_result_'+time stamp+one random number)
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114
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115 -c <flag> (if '-c' was flagged, SeqSero2S will only output serotype prediction without the directory containing log files)
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116
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117 -n <string> (optional, to specify a sample name in the report output)
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118
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119 -s <flag> (if '-s' was flagged, SeqSero2S will not output header in SeqSero_result.tsv)
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120
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121 --check <flag> (use '--check' flag to check the required dependencies)
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122
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123 -v, --version (show program's version number and exit)
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124
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125
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126 # Examples
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127 Allele mode:
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128
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129 # Allele workflow ("-m a", default), for separated paired-end raw reads ("-t 2"), use 10 threads in mapping and assembly ("-p 10")
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130 SeqSero2S.py -p 10 -t 2 -i R1.fastq.gz R2.fastq.gz
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131
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132 K-mer mode:
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133
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134 # Raw reads k-mer ("-m k"), for separated paired-end raw reads ("-t 2")
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135 SeqSero2S.py -m k -t 2 -i R1.fastq.gz R2.fastq.gz
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136
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137 # Genome assembly k-mer ("-t 4", genome assemblies only predicted by the k-mer workflow, "-m k")
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138 SeqSero2S.py -m k -t 4 -i assembly.fasta
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139
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140 # Output
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141 Upon executing the command, a directory named 'SeqSero_result_Time_your_run' will be created. Your result will be stored in 'SeqSero_result.txt' in that directory. And the assembled alleles can also be found in the directory if using "-m a" (allele mode).
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142
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143
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144 # Citation
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145 Zhang S, Den-Bakker HC, Li S, Dinsmore BA, Lane C, Lauer AC, Fields PI, Deng X.
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146 SeqSero2: rapid and improved Salmonella serotype determination using whole genome sequencing data.
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147 **Appl Environ Microbiology. 2019 Sep; 85(23):e01746-19.** [PMID: 31540993](https://aem.asm.org/content/early/2019/09/17/AEM.01746-19.long)
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148
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149 Zhang S, Yin Y, Jones MB, Zhang Z, Deatherage Kaiser BL, Dinsmore BA, Fitzgerald C, Fields PI, Deng X.
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150 Salmonella serotype determination utilizing high-throughput genome sequencing data.
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151 **J Clin Microbiol. 2015 May;53(5):1685-92.** [PMID: 25762776](http://jcm.asm.org/content/early/2015/03/05/JCM.00323-15)