NAME

       Bio::Tradis::Map - Perform mapping

VERSION

       version 1.4.5

SYNOPSIS

       Takes a reference genome and indexes it.  Maps given fastq files to ref.

          use Bio::Tradis::Map;

          my $pipeline = Bio::Tradis::Map->new(fastqfile => 'abc', reference => 'abc');
          $pipeline->index_ref();
          $pipeline->do_mapping();

PARAMETERS

   Required
       ·   "fastqfile" - path to/name of file containing reads to map to the reference

       ·   "reference" - path to/name of reference genome in fasta format (.fa)

   Optional
       ·   "refname" - name to assign to the reference index files. Default = ref.index

       ·   "outfile" -  name to assign to the mapped SAM file. Default = mapped.sam

METHODS

       ·   "index_ref" - create index files of the reference genome. These are required
                          for the mapping step. Only skip this step if index files already
                          exist. -k and -s options for referencing are calculated based
                          on the length of the reads being mapped as per table:

       ·   "do_mapping" - map "fastqfile" to "reference". Options used for mapping are: "-r -1 -x
           -y 0.96"

       For more information on the mapping and indexing options discussed here, see the SMALT
       manual <ftp://ftp.sanger.ac.uk/pub4/resources/software/smalt/smalt-manual-0.7.4.pdf>

AUTHOR

       Carla Cummins <path-help@sanger.ac.uk>

COPYRIGHT AND LICENSE

       This software is Copyright (c) 2013 by Wellcome Trust Sanger Institute.

       This is free software, licensed under:

         The GNU General Public License, Version 3, June 2007