Bio::Tradis::Map - Perform mapping
version 1.4.5
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();
fastqfile - path to/name of file containing reads to map to the reference
fastqfile
reference - path to/name of reference genome in fasta format (.fa)
reference
refname - name to assign to the reference index files. Default = ref.index
refname
outfile - name to assign to the mapped SAM file. Default = mapped.sam
outfile
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:
index_ref
do_mapping - map fastqfile to reference. Options used for mapping are: -r -1 -x -y 0.96
do_mapping
-r -1 -x -y 0.96
For more information on the mapping and indexing options discussed here, see the SMALT manual
Carla Cummins <path-help@sanger.ac.uk>
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
To install Bio::Tradis, copy and paste the appropriate command in to your terminal.
cpanm
cpanm Bio::Tradis
CPAN shell
perl -MCPAN -e shell install Bio::Tradis
For more information on module installation, please visit the detailed CPAN module installation guide.