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CFSAN-Biostatistics / shigatyper

CFSAN Shigella Typing Pipeline
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ShigaTyper

ShigaTyper is a quick and easy tool designed to determine Shigella serotype using Illumina (single or paired-end) or Oxford Nanopore reads with low computation requirement.

Installation

Shigatyper is available from Bioconda and can be installed using the following command.

conda create -n shigatpyer -c conda-forge -c bioconda shigatyper

Running ShigaTyper

ShigaTyper supports compressed FASTQs as inputs. These FASTQs can be single-end or paired-end Illumina reads, or reads from Oxford Nanopore.

usage: shigatyper.py [-h] [--R1 FASTA] [--R2 FASTA] [--SE FASTA] [--ont] [-n SAMPLE_NAME] [--verbose] [--version]

ShigaTyper v. 2.0.2, 2022

options:
  -h, --help            show this help message and exit
  --R1 FASTA            Input FASTQ is R1 of paired-end reads
  --R2 FASTA            Input FASTQ is R2 of paired-end reads
  --SE FASTA            Input FASTQ is contains single-end reads
  --ont                 The input FASTQ file contains ONT reads
  -n SAMPLE_NAME, --name SAMPLE_NAME
  --verbose, -v
  --version             show program's version number and exit

Example Runs

# 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 +

ShigaTyper Outputs

After your run is complete, two tab-delimited TSV files (<PREFIX>.tsv and <PREFIX>-hits.tsv) are created with the results. By default the output files, uses the base name of the input FASTQ file. You can change this by using the --name parameter.

Example <PREFIX>.tsv

This file contains the final serotype predicted by ShitaTyper. It looks like the following:

# With A predicted Serotype
sample  prediction  ipaB    notes
SRX7050861-ont  Shigella dysenteriae serotype 3 +   this strain is ipaB+, suggesting that it retains the virulent invasion plasmid.

# Note Shigella or EIEC
sample  prediction  ipaB    notes
ERR3772599  Not Shigella or EIEC    -   No read was mapped to the reference sequence database.

The <PREFIX>.tsv will have the following four collumns.

Column Name Description
sample The name of the input sample
prediction The serotype predicted by ShigaTyper
ipaB The precence of ipaB (+) or absence (-)
notes Any notes associated with result

Example <PREFIX>-hits.tsv

The <PREFIX>-hits.tsv file will contain statistics about each individual gene hit. If there are no hits, this file will not be produced (e.g. non-Shigella or EIEC inputs).

Here's an example of how it will look:

    Hit Number of reads Length Covered  reference length    % covered   Number of variants  % accuracy
0   ipaH_c  331 780 780 100.0   10  98.7
1   ipaB    59  1743    1743    100.0   44  97.5
2   Sd3_wzx 18  1515    1515    100.0   7   99.5
3   Sd3_wzy 20  1104    1104    100.0   3   99.7
Column Name Description
index Index number in the array
Hit Name of the gene
Number of reads Number of reads mapped to the Hit
Length Covered Length of reference gene aligned to
reference length Length of the reference gene
% covered Percent of the reference gene aligned to
Number of variants Number of varaints in the alignment
% accuracy Percent of identical matches across the reference gene

Citations

If you make use of this tool, please cite the following: