Search other typing profile of a strain

In complement to classical MSLT, you can search for other typing METHOD using a draft genome or raw reads.

Typing method

fimH typing

FimH typing is based on the allelic sequence of the fimH gene in the species Escherichia coli (Dias et al, 2010). Allelic sequence were download from CGE.

spa typing

Spa typing is based on the repetitions polymorphism present on the protein A gene (spa) in the species Staphylococcus aureus (Frénay et al, 1996). Repetitions and sequence types definition were download from Ridom.

Clermont typing

Clermont phylogrouping is based on the presence/absence of 4 different genes in the species Escherichia coli (Clermont et al, 2012).

Genome data

You can search typing METHOD from GENOME fasta sequence files.

pyTyper search --help
Usage: pyTyper search [OPTIONS] {fim|spa|clmt} GENOMES...

Searches strain type using specified METHOD for an assembly GENOME.

fim: fimH typing for Escherichia coli
spa: spa typing for Staphylococcus aureus
clmt: Phylogouping using ClermontTyping method for Escherichia coli

Options:
-i, --identity FLOAT   Minimum identity to search gene.
-c, --coverage FLOAT   Minimum coverage to search gene.
-f, --fasta FILENAME   Writes fasta file with gene allele.
-o, --output FILENAME  Writes search result to (default:stdout).

Note

If new alleles are present or you want to have sequence target by the typing method in your strains, you can obtain their sequences with the -f option.

Note

You can perform searches on multiple genomes simultaneously.