---
name: "Bio::Tradis::Map"
section: "3pm"
platform: "linux"
package: "bio-tradis"
version: "1.4.5+dfsg2-2"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/Bio::Tradis::Map"
---

# Bio::Tradis::Map(3pm)

Perform mapping

## 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
```