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.
Shigatyper is available from Bioconda and can be installed using the following command.
conda create -n shigatpyer -c conda-forge -c bioconda 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
# 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 +
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.
<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 |
<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 |
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)