Bio::Tradis::Map - Perform mapping

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

perl v5.38.2                                       2024-01-25                              Bio::Tradis::Map(3pm)

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>

Name

       Bio::Tradis::Map - Perform 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

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();