ShigEiFinder

This is a tool that is used to identify differentiate Shigella/EIEC using cluster-specific genes and identify the serotype using O-antigen/H-antigen genes. This pipeline can serotype over 59 Shigella and 22 EIEC serotypes using either assembled whole genomes or Whole Genome Sequencing (WGS) reads. The results are output in a tabular format which if saved as a file can be opened in Excel or other tabular programs. Also available as an online tool and published in microbial genomics.

Example:

#SAMPLE     ipaH  VIRULENCE_PLASMID  CLUSTER  SEROTYPE  O_ANTIGEN  H_ANTIGEN  NOTES
ERR1000679  +     1                  CSD1     SD1       SD1

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Installation

Dependencies

1. samtools (v1.10)
2. Python (v3.7.3 or above)
3. bwa (v0.7.17-r1188)
4. BLAST+ (v2.9.0)

Option 1: Clone repository from GitHub

git clone https://github.com/LanLab/ShigEiFinder.git

cd ShigEiFinder

python setup.py install

Make sure that you have the dependencies installed.

Option 2: Conda installation

conda install -c conda-forge -c bioconda shigeifinder

Option 3: Docker Images/Containers

1. Bioconda/Biocontainer docker images: https://quay.io/repository/biocontainers/shigeifinder?tab=tags

# download the docker image to your machine
docker pull quay.io/biocontainers/shigeifinder:1.3.4--pyhdfd78af_0

# view help options
docker run quay.io/biocontainers/shigeifinder:1.3.4--pyhdfd78af_0 shigeifinder --help

2. Third-party docker images from the StaPH-B working group:

• Dockerhub: https://hub.docker.com/r/staphb/shigeifinder/tags
• Quay: https://quay.io/repository/staphb/shigeifinder?tab=tags
  • Note: docker images hosted on StaPH-B's dockerhub & quay repos are identical, you can use either.
• Dockerfiles & documentation on docker images: https://github.com/StaPH-B/docker-builds/tree/master/shigeifinder
• ⚠️ We cannot provide support for StaPH-B docker images, please file a GitHub Issue here if you need help or run into issues.

# download the docker image to your machine
docker pull staphb/shigeifinder:latest

# view help options
docker run staphb/shigeifinder:latest shigeifinder --help

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Usage

For genomes (FASTA files):

shigeifinder -i <inputs>...

For raw reads:

shigeifinder -r -i <read1> <read2>...

Parameters Description

• -h, --help: show this help message and exit
• -i: Input files list provided with their paths. Either genomes or read files can be used
• -r: Used to indicate that raw read files are input. Make sure that the reads are put in the order of read1 and then read2
• -t: number of threads used. The default is 4.
• --single_end: Add flag if raw reads are single end rather than paired.
• --hits: provides the genes set that was used to identify the cluster and serotype as well as the original BLAST/mapping results.
• --dratio: displays the depth ratio of the depth of the cluster genes to the average depth of 7 HK genes
• --update_db: updating the intermediate files for the genes database when new gene sequences have been added to the FASTA file
• --output: output file to write to (if not used writes to stdout)
• --check: check that dependencies are found in path
• --o_depth: When using reads as input the minimum depth percentage relative to genome average for positive O antigen gene call (default 1)
• --ipaH_depth: When using reads as input the minimum depth percentage relative to genome average for positive ipaH gene call (default 1)
• --depth: When using reads as input the minimum read depth for non ipaH/Oantigen gene to be called (default 10)
• --tmpdir TMPDIR: Temporary folder to use for intermediate files.
• --noheader: Do not print output header.
• -v, --version: Print version information. Example: shigeifinder 1.3.5

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Troubleshooting

• If there is an error where there are no genes being mapped, there might be not enough memory given to the machine. Try giving more memory.