Awesome
legsta
In silico Legionella pneumophila Sequence Based Typing (SBT)
Background
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.
Install
Conda
conda install -c conda-forge -c bioconda -c defaults legsta
Homebrew
brew install brewsci/bio/legsta
Github
cd $HOME
git clone https://github.com/tseemann/legsta.git
cd $HOME/legsta/test
../bin/legsta *.fna *.gbk
Input
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
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 ?
Options
| Option | Description |
|---|---|
--quiet | do not print any informational messages to stderr |
--csv | comma-separated output instead of tab-separated |
--noheader | don't print table header to output (ie. FILE SBT flaA ...) |
--version | print legsta X.Y.Z version to stdout and exit |
Dependencies
Issues
Submit questions or issues to our Issue Tracker
Authors
- Torsten Seemann
- Anders Goncalves Da Silva
- Andrew Buultjens
- Jason Kwong
Licence
Acknowledgements
- Natalie Groves for providing the latest sequences and profiles from the PHE database