ShigaTyper is a quick and easy tool designed to determine Shigella serotype using Illumina paired end reads with low computation requirement. It has been tested on an Ubuntu 16.04.3 LTS guest addition on VMware Player version 14.1.1 in a Windows 7 and Virtual Box version 5.2.4 in a Windows 10 operating system.
usage: shigatyper [-h] [-n SAMPLE_NAME] [--verbose] [--version] read1 read2
positional arguments:
read1
read2
optional arguments:
-h, --help show this help message and exit
-n SAMPLE_NAME, --name SAMPLE_NAME
--verbose, -v
--version show program's version number and exit
$ shigatyper.py CFSAN029786_S10_L001_R1_001.fastq.gz CFSAN029786_S10_L001_R2_001.fastq.gz
sample prediction ipaB
CFSAN029786 Shigella dysenteriae serotype 3 +