README.md

Shigatyper 2.0.5 container

Main tool : shigatyper

Additional tools:

• samtools 1.9
• bcftools 1.9
• minimap2 2.24
• python 3.10.6

Example Usage

# Paired-end reads
shigatyper.py --R1 SRX5006488_R1.fastq.gz --R2 SRX5006488_R2.fastq.gz
sample  prediction      ipaB
SRX5006488      Shigella boydii serotype 12     +

# Single-end reads
shigatyper.py --SE SRX5006488.fastq.gz
sample  prediction      ipaB
SRX5006488-se   Shigella boydii serotype 12     +

# Oxford Nanopore reads
shigatyper.py --SE SRX7050861.fastq.gz --ont
sample  prediction      ipaB
SRX7050861-ont  Shigella dysenteriae serotype 3 +

Better documentation can be found at https://github.com/CFSAN-Biostatistics/shigatyper