SeqSero2 alpha-test version

Salmonella serotyping from genome sequencing data

Introduction

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.

Dependencies

SeqSero has two modes:

(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 and [SalmID] (https://github.com/hcdenbakker/SalmID).

K-mer mode is a independant pipeline, it only requires:

Python 3;
SRA Toolkit (optional, just used to fastq-dump sra files);

(B) allele based mode (if users want to extract serotype determinant alleles), which applies a hybrid approach of reads-mapping and micro-assembly.

Allele mode depends on:

Executing the code

Usage: SeqSero2_package.py 

-m <string> (which mode to apply, 'k'(kmer mode), 'a'(allele mode), default=k)

-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)

-i <file> (/path/to/input/file)

-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) 

-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)

-d <string> (output directory name, if not set, the output directory would be 'SeqSero_result_'+time stamp+one random number)

-c <flag> (if '-c' was flagged, SeqSero2 will use clean mode and only output serotyping prediction without the directory containing log files)

Examples

K-mer mode:

# K-mer (default), for separated paired-end raw reads ("-t 2")
SeqSero2_package.py -t 2 -i R1.fastq.gz R2.fastq.gz

# K-mer (default), for assemblies ("-t 4", assembly only predcited by K-mer mode)
SeqSero2_package.py -t 4 -i R1.fastq.gz R2.fastq.gz

Allele mode:

# Allele mode ("-m a"), for separated paired-end raw reads ("-t 2"), use 10 threads in mapping and assembly ("-p 10")
SeqSero2_package.py -m a -p 10 -t 2 -i R1.fastq.gz R2.fastq.gz

Output

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).

Citation

Zhang S, Yin Y, Jones MB, Zhang Z, Deatherage Kaiser BL, Dinsmore BA, Fitzgerald C, Fields PI, Deng X.
Salmonella serotype determination utilizing high-throughput genome sequencing data.
J Clin Microbiol. 2015 May;53(5):1685-92.PMID:25762776

chen1i6c04 / SeqSero2