2.0.4

Shigatyper 2.0.4 container

Main tool : shigatyper

Additional tools:

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

Known Version Issue

The 2.0.4 release of Shigatyper reports the incorrect version 2.0.3 when running shigatyper --version. This is a known issue and should be addressed in the next version release. Users should not rely upon the command for correctly reporting the version, but rather the docker image tag 2.0.4 for tracking the correct version.

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