In silico Legionella pneumophila Sequence Based Typing (SBT)

SBT stands for sequence-based typing. The purpose of the Legionella pneumophila SBT scheme is to provide a rapid and easily comparable method for the epidemiological typing of clinical and environmental isolates of Legionella pneumophila in outbreak investigations.

conda install -c conda-forge -c bioconda -c defaults legsta

The any2fasta tool is used to convert input files to FASTA for feeding to isPcr. It can accept FASTA, Genbank, EMBL, GFF, and many other formats. The files may also be compressed with gzip, bzip2 or zip.

Output is a TSV file (or CSV if --csv is used). Alleles with no in silico product are denoted - and novel alleles listed using ?.

% cd legsta/test
% ../bin/legsta NC_006368.fna NC_018140.fna CR628336.1.gbk.gz missing_flaA.fna FJBS01000000.fna.bz2


FILE  		       SBT     flaA    pilE    asd     mip     mompS   proA    neuA
NC_006368.fna          1       1       4       3       1       1       1       1
NC_018140.fna          734     2       6       17      1       1       8       11
CR628336.1.gbk.gz      1       1       4       3       1       1       1       1
missing_flaA.fna       -       -       14      16      25      7       13      206
FJBS01000000.fna.bz2   -       3       10      1       3       14      9       ?

Submit questions or issues to our Issue Tracker

• Torsten Seemann
• Anders Goncalves Da Silva
• Andrew Buultjens
• Jason Kwong

GPLv3

Natalie Groves for providing the latest sequences and profiles from the PHE database

• Public Health England - L.pneumophila SBT Home Page
• Gaia et al (2005)
• Ratzow et al (2007)