NAME

get_emm_sequence_type - Given an assembly find the MLST sequence type of the emm gene from the CDC.

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.

   # Basic usage, sequence type result written to my_assembly.fa.st
   get_emm_sequence_type my_assembly.fa

   # Multiple fasta files
   get_emm_sequence_type myfasta.fa anotherfasta.fa yetanother.fa

   # Split into 8 parallel processes (much faster), default is 2
   get_emm_sequence_type -d 8 *.fa

   # output a fasta file with the concatenated alleles and unknown sequences
   get_emm_sequence_type -c  my_assembly.fa

   # output a phylip file with the concatenated alleles and unknown sequences
   get_emm_sequence_type -y  my_assembly.fa

   # Specify an output directory
   get_emm_sequence_type  -o /path/to/results my_assembly.fa

   # This help message
   get_emm_sequence_type -h

   # print version
   get_emm_sequence_type -v

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