NAME

    Bio::MLST::Check - Multilocus sequence type checking using blast

VERSION

    version 2.1.1706216

SYNOPSIS

    High throughput multilocus sequence typing (MLST) checking.

DESCRIPTION

    This application is for taking Multilocus sequence typing (MLST)
    sources from multiple locations and consolidating them in one place so
    that they can be easily used (and kept up to date). Then you can
    provide FASTA files and get out sequence types for a given MLST
    database. Two spreadsheets are outputted, one contains the allele
    number for each locus, and the ST (or nearest ST), the other contains
    the genomic sequence for each allele. If more than 1 allele gives 100%
    identity for a locus, the contaminated flag is set. Optionally you can
    output a concatenated sequence in FASTA format, which you can then use
    with tree building programs. New, unseen alleles are saved in FASTA
    format, with 1 per file, for submission to back to MLST databases.

    It requires NCBI Blast+ to be installed and for blastn and makeblastdb
    to be in your PATH.

       # Add this environment variable to your ~/.bashrc file - do this once
       export MLST_DATABASES=/path/to/where_you_want_to_store_the_databases
       
       # Download the latest copy of the databases (run it once per month)
       download_mlst_databases
       
       # Find the sequence types for all fasta files in your current directory
       get_sequence_type -s "Clostridium difficile" *.fa
    
       use Bio::MLST::Check;
       Bio::MLST::Check->new(
         'species'           => 'E.coli',
         'base_directory'    => '/path/to/dir',
         'raw_input_fasta_files'  => ['myfasta.fa'],
         'makeblastdb_exec'  => 'makeblastdb',
         'blastn_exec'       => 'blastn',
         'output_directory'  => '/path/to/output',
         'output_fasta_files'=> 1,
       );

METHODS

 create_result_files

    Creates a spreadsheet of results, FASTA files with novel sequences and
    optionally a concatentated sequence (FASTA) for tree building.

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