admiralenola / stx_subtyping

stx_subtyping: a tool for subtyping shiga toxin genes from fastqs or fastas.

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