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.\" ========================================================================
.\"
.IX Title "Bio::Tradis::Map 3pm"
.TH Bio::Tradis::Map 3pm "2020-01-11" "perl v5.30.0" "User Contributed Perl Documentation"
.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
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.SH "NAME"
Bio::Tradis::Map \- Perform mapping
.SH "VERSION"
.IX Header "VERSION"
version 1.4.5
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
Takes a reference genome and indexes it.
Maps given fastq files to ref.
.PP
.Vb 1
\&   use Bio::Tradis::Map;
\&   
\&   my $pipeline = Bio::Tradis::Map\->new(fastqfile => \*(Aqabc\*(Aq, reference => \*(Aqabc\*(Aq);
\&   $pipeline\->index_ref();
\&   $pipeline\->do_mapping();
.Ve
.SH "PARAMETERS"
.IX Header "PARAMETERS"
.SS "Required"
.IX Subsection "Required"
.IP "\(bu" 4
\&\f(CW\*(C`fastqfile\*(C'\fR \- path to/name of file containing reads to map to the reference
.IP "\(bu" 4
\&\f(CW\*(C`reference\*(C'\fR \- path to/name of reference genome in fasta format (.fa)
.SS "Optional"
.IX Subsection "Optional"
.IP "\(bu" 4
\&\f(CW\*(C`refname\*(C'\fR \- name to assign to the reference index files. Default = ref.index
.IP "\(bu" 4
\&\f(CW\*(C`outfile\*(C'\fR \-  name to assign to the mapped \s-1SAM\s0 file. Default = mapped.sam
.SH "METHODS"
.IX Header "METHODS"
.IP "\(bu" 4
\&\f(CW\*(C`index_ref\*(C'\fR \- 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:
.IP "\(bu" 4
\&\f(CW\*(C`do_mapping\*(C'\fR \- map \f(CW\*(C`fastqfile\*(C'\fR to \f(CW\*(C`reference\*(C'\fR. Options used for mapping are: \f(CW\*(C`\-r \-1 \-x \-y 0.96\*(C'\fR
.PP
For more information on the mapping and indexing options discussed here, see the \s-1SMALT\s0 manual <ftp://ftp.sanger.ac.uk/pub4/resources/software/smalt/smalt-manual-0.7.4.pdf>
.SH "AUTHOR"
.IX Header "AUTHOR"
Carla Cummins <path\-help@sanger.ac.uk>
.SH "COPYRIGHT AND LICENSE"
.IX Header "COPYRIGHT AND LICENSE"
This software is Copyright (c) 2013 by Wellcome Trust Sanger Institute.
.PP
This is free software, licensed under:
.PP
.Vb 1
\&  The GNU General Public License, Version 3, June 2007
.Ve