NOTE: I have cloned this from https://github.com/flashton2003/stx_subtyping
Installation
pip install git+https://github.com/AdmiralenOla/stx_subtyping
Requirements
Tested with Biopython v1.6.3
Test with pysam v0.6
Bowtie2
Need to have bowtie2 installed and available in your PATH (i.e. when you type bowtie2 from any location, it runs bowtie2)
Useage
stx_subtyping -h stx_subtyping dual_stx_subtyping -h
stx_subtyping dual_stx_subtyping /path/to/fastq1.fastq /path/to/fastq2.fastq /path/to/contigs.fa /path/to/whereyouwanttheoutput
There are 3 running options. The best approach is dual_stx_subtyping, but if only fastqs or fastas are available, the other options can be used.
dual_stx_subtyping - Takes a pair of fastqs and a set of contigs for a strain, outputs info into output_dir
assblast_only - Use this when you only have contigs
mapsnp_only - Use this when you only have fastqs, no assemblies
If in doubt, try -h