Streptofile

Group A Streptococcus (Streptococcus pyogenes) profiling from whole genome sequencing data

Current version of Streptofile performs

• EMM typing based on the emm nucleotide sequence database curated by the U.S. Centers for Disease Control and Prevention (https://ftp.cdc.gov/pub/infectious_diseases/biotech/tsemm/)
• Multilocus Sequence Typing based on the S. pyogenes scheme curated by pubMLST (https://pubmlst.org/bigsdb?db=pubmlst_spyogenes_seqdef)
• Virulence gene profiling based on 66 known virulence factors

Setup

Conda install

conda install thej-ssi::streptofile

pip install

pip install streptofile

non-python dependencies that need to be installed:

• blast

Usage

To run emm typing, MLST and virulence gene detection on a batch of assembly files

streptofile -o <output_folder> *.fasta

To run only a subset of analyses, these can be specified in a comma-separated list using the --analyses parameter

streptofile -o <output_folder> --analyses emm,mlst,virulence *.fasta

Input

Designed for genome assemblies, though all nucleotide fasta input will work, so cds files or similar is fine as well

Outputs

• <output_folder>/results.tsv: All analysis results in a wide table format. Includes emm-typing results, mlst results and one column for each of the 66 virulence genes indicating presence or absence of that gene.
• <output_folder>/virulence_details.tsv: All identified virulence genes in long table format. Includes information on coverage, identity, sequence reference and the identified sequence
• <output_fodler>/<sample_name>: One folder for each input fasta with blast results etc.