get_sequence_type - Given an assembly find the MLST sequence type.
version 2.1.1706216
Given Fasta files and a Species regex, lookup the relevant MLST database and output the sequence type to a file. It requires NBCI Blast+ to be available in your PATH.
Usage: get_sequence_type [options] *.fasta
-s STR Species of MLST scheme (0 or more comma separated) -d INT Number of threads [1] -c Output a FASTA file of concatenated alleles and unknown sequences -y Output a phylip file of concatenated alleles and unknown sequences -o STR Output directory [.] -a Print out all available MLST schemes and exit -h Print this message and exit -v Print version number and exit
Andrew J. Page <ap13@sanger.ac.uk>
This software is Copyright (c) 2012 by Wellcome Trust Sanger Institute.
This is free software, licensed under:
The GNU General Public License, Version 3, June 2007
To install Bio::MLST::Check, copy and paste the appropriate command in to your terminal.
cpanm
cpanm Bio::MLST::Check
CPAN shell
perl -MCPAN -e shell install Bio::MLST::Check
For more information on module installation, please visit the detailed CPAN module installation guide.