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1 # SeqSero2 alpha-test version
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2 Salmonella serotyping from genome sequencing data
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3
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4
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5 # Introduction
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6 SeqSero2 is a pipeline for Salmonella serotype determination from raw sequencing reads or genome assemblies. This is a alpha test version. A web app will be available soon.
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7
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8
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9 # Dependencies
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10 SeqSero has two modes:
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11
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12
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13 (A) k-mer based mode (default), which applies unique k-mers of serotype determinant alleles to determine Salmonella serotypes in a fast speed. Special thanks to Dr. Hendrik Den Bakker for his significant contribution to this mode, details can be found in [SeqSeroK](https://github.com/hcdenbakker/SeqSeroK) and [SalmID](https://github.com/hcdenbakker/SalmID).
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14
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15 K-mer mode is a independant pipeline, it only requires:
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16
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17 1. Python 3;
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18 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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19
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20
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21 (B) allele based mode (if users want to extract serotype determinant alleles), which applies a hybrid approach of reads-mapping and micro-assembly.
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22
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23 Allele mode depends on:
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24
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25 1. Python 3;
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26
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27 2. [Burrows-Wheeler Aligner](http://sourceforge.net/projects/bio-bwa/files/);
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28
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29 3. [Samtools](http://sourceforge.net/projects/samtools/files/samtools/);
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30
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31 4. [NCBI BLAST](https://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE_TYPE=BlastDocs&DOC_TYPE=Download);
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32
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33 5. [SRA Toolkit](http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd=show&f=software&m=software&s=software);
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34
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35 6. [SPAdes](http://bioinf.spbau.ru/spades);
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36
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37 7. [Bedtools](http://bedtools.readthedocs.io/en/latest/);
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38
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39 8. [SalmID](https://github.com/hcdenbakker/SalmID).
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40
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41
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42 # Executing the code
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43 Make sure all SeqSero2 and its dependency executables are added to your path (e.g. to ~/.bashrc). Then type SeqSero2_package.py to get detailed instructions.
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44
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45 Usage: SeqSero2_package.py
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46
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47 -m <string> (which mode to apply, 'k'(kmer mode), 'a'(allele mode), default=k)
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48
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49 -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 fasta, '6'for nanopore fastq)
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50
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51 -i <file> (/path/to/input/file)
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52
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53 -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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54
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55 -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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56
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57 -d <string> (output directory name, if not set, the output directory would be 'SeqSero_result_'+time stamp+one random number)
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58
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59 -c <flag> (if '-c' was flagged, SeqSero2 will use clean mode and only output serotyping prediction without the directory containing log files)
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60
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61
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62 # Examples
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63 K-mer mode:
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64
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65 # K-mer (default), for separated paired-end raw reads ("-t 2")
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66 SeqSero2_package.py -t 2 -i R1.fastq.gz R2.fastq.gz
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67
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68 # K-mer (default), for assemblies ("-t 4", assembly only predcited by K-mer mode)
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69 SeqSero2_package.py -t 4 -i assembly.fasta
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70
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71 Allele mode:
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72
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73 # Allele mode ("-m a"), for separated paired-end raw reads ("-t 2"), use 10 threads in mapping and assembly ("-p 10")
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74 SeqSero2_package.py -m a -p 10 -t 2 -i R1.fastq.gz R2.fastq.gz
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75
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76
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77 # Output
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78 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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79
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80
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81 # Citation
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82 Zhang S, Yin Y, Jones MB, Zhang Z, Deatherage Kaiser BL, Dinsmore BA, Fitzgerald C, Fields PI, Deng X.
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83 Salmonella serotype determination utilizing high-throughput genome sequencing data.
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84 **J Clin Microbiol.** 2015 May;53(5):1685-92.[PMID:25762776](http://jcm.asm.org/content/early/2015/03/05/JCM.00323-15)
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