kapsakcj / shigatyper

CFSAN Shigella Typing Pipeline

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:

• ShigaTyper
  This tool, for serotyping Shigella. Wu Y, Lau HK, Lee T, Lau DK, Payne J In Silico Serotyping Based on Whole-Genome Sequencing Improves the Accuracy of Shigella Identification. Applied and Environmental Microbiology, 85(7). (2019)

• BCFtools
  Utilities for variant calling and manipulating VCFs and BCFs.
  Danecek P, Bonfield JK, Liddle J, Marshall J, Ohan V, Pollard MO, Whitwham A, Keane T, McCarthy SA, Davies RM, Li H Twelve years of SAMtools and BCFtools GigaScience Volume 10, Issue 2 (2021)

• Minimap2
  A versatile pairwise aligner for genomic and spliced nucleotide sequences
  Li H Minimap2: pairwise alignment for nucleotide sequences. Bioinformatics 34:3094-3100 (2018)

• Samtools
  Tools for manipulating next-generation sequencing data
  Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R The Sequence Alignment/Map format and SAMtools. Bioinformatics 25, 2078–2079 (2009)