NAME

Bio::Tradis::Map - Perform mapping

VERSION

version 1.4.1

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:

  Read length	k	s
  <70	13	4
  >70 and <100	13	6
  >100	20	6

• 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

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