#mlst
Scan contig files against PubMLST typing schemes.
##Installation
The main Perl script and the included databases:
% cd $HOME
% git clone https://github.com/Victorian-Bioinformatics-Consortium/mlst.git
The only external dependency is the BLAT tools written by Jim Kent: http://genome.ucsc.edu/FAQ/FAQblat.html#blat3
% cd $HOME/mlst/bin
# Linux:
% wget http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/blat/blat
# MacOSX:
% wget http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/blat
% chmod +x blat
Add it to your PATH:
% echo "export PATH=$PATH:$HOME/mlst/bin" >> $HOME/.bashrc
Now log out, and log back in, and test that it works:
% mlst -h
% blat
Success!
##Usage
###Available schemes
To see which PubMLST schemes are supported:
% mlst --list
abaumannii achromobacter aeromonas afumigatus cdifficile efaecium
haemophilus hcinaedi hparasuis hpylori kpneumoniae leptospira
saureus xfastidiosa yersinia ypseudotuberculosis yruckeri
The above list is shortened. The full included database includes 106 schemes.
###Genotyping one genome
To genotype a FASTA file of contigs:
% mlst --scheme saureus USA300.fasta
FILE SCHEME ST arcc aroe glpf gmk_ pta_ tpi_ yqil
USA300.fasta saureus 8 3 3 1 1 4 4 3
This produces a tab-separated values file, with a header line and a line for the FASTA file. The "ST" column is the MLST type, and the subsequent columns are the allele variants for each of the locii within the scheme. In this case, the USA300 genome is Staphylococcus aureus ST8.
Only full-length, 100% identity matches to an allelle are considered matches. If any allelles are not found, a "-" will be present in the allele column, as well as in the ST column.
###Genotyping many genomes
The software supports multiple genome FASTA files, even compressed ones.
% mlst --scheme efaecium VAN*.fna.gz
FILE SCHEME ST AtpA Ddl Gdh PurK Gyd PstS Adk
VAN_219 efaecium 784 2 3 1 67 1 30 25
VAN_222 efaecium 784 2 3 1 67 1 30 25
VAN_327 efaecium 417 5 7 5 7 2 1 1
VAN_332 efaecium 38 2 5 3 5 4 4 1
VAN_335 efaecium 417 5 7 5 7 2 1 1
VAN_342 efaecium 22 2 3 1 2 1 1 1
VAN_345 efaecium 38 2 5 3 5 4 4 1
VAN_476 efaecium 785 2 3 1 67 1 86 1
###Tweaking the output
The output is TSV (tab-separated values). This makes it easy to parse and manipulate with Unix utilities like cut and sort etc. For example, if you only want the filename and ST you can do the following:
% mlst --scheme abaumanii AB*.fasta | cut -f1,3 > ST.tsv
If you don't want the header line use the --noheader option:
% mlst --scheme leptospira --noheader L550.fa
If you prefer CSV because it loads more smoothly into MS Excel, use the --csv option:
% mlst --scheme hpylori --csv Peptobismol.fna.gz > mlst.csv
##Bugs
Please submit via the Github Issues page: https://github.com/Victorian-Bioinformatics-Consortium/mlst/issues
##Licence
GPLv2
##Author
Torsten Seemann - http://vicbioinformatics.com/