NAME

get_sequence_type - Given an assembly find the MLST sequence type.

VERSION

version 2.1.1706216

SYNOPSIS

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

AUTHOR

Andrew J. Page <ap13@sanger.ac.uk>

COPYRIGHT AND LICENSE

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