NAME

get_sequence_type - Given an assembly find the MLST sequence type.

VERSION

version 1.130160

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_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 
   
   # 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

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