NAME

get_sequence_type - Given an assembly find the MLST sequence type.

VERSION

version 2.1.1534813

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

# 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

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