get_sequence_type - Given an assembly find the MLST sequence type.
version 2.1.1630713
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.
# Basic usage, sequence type result written to my_assembly.fa.st get_sequence_type -s "Clostridium difficile" my_assembly.fa # Multiple fasta files get_sequence_type -s "Clostridium difficile" myfasta.fa anotherfasta.fa yetanother.fa # or get_sequence_type -s "Clostridium difficile" *.fa # Split into 8 parallel processes (much faster), default is 2 get_sequence_type -s "Clostridium difficile" -d 8 *.fa # output a fasta file with the concatenated alleles and unknown sequences get_sequence_type -s "Clostridium difficile" -c my_assembly.fa # output a phylip file with the concatenated alleles and unknown sequences get_sequence_type -s "Clostridium difficile" -y my_assembly.fa # Specify an output directory get_sequence_type -s "Clostridium difficile" -o /path/to/results my_assembly.fa # Match against multiple MLST databases get_sequence_type -s "Clostridium botulinum, Clostridium difficile" my_assembly.fa # Match against all MLST databases get_sequence_type my_assembly.fa # list all available MLST databases get_sequence_type -a # This help message get_sequence_type -h # print version get_sequence_type -v
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.