Description

A method to improve mappings on circular genomes, using the BWA mapper.

Input

name:type
description
pattern

meta{:bash}

:map

Groovy Map containing reference information e.g. [ id:'sample1' ]

reference{:bash}

:file

Genome fasta file

*.fasta

meta2{:bash}

:map

Groovy Map containing reference information e.g. [ id:'sample1' ]

elongation_factor{:bash}

:integer

The number of bases that the ends of the target chromosome in the reference genome should be elongated by

meta3{:bash}

:map

Groovy Map containing reference information e.g. [ id:'sample1' ]

target{:bash}

:string

The name of the chromosome in the reference genome that should be elongated

Output

name:type
description
pattern

fasta{:bash}

meta{:bash}

:map

Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]

*_${elongation_factor}.fasta{:bash}

:file

Genome fasta file

*.fasta

elongated{:bash}

meta{:bash}

:map

Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]

*${elongation_factor}_elongated{:bash}

:file

File listing the chromosomes that were elongated

*_elongated

versions{:bash}

versions.yml{:bash}

:file

File containing software versions

versions.yml

Tools

circulargenerator
GPL v3

Creating a modified reference genome, with an elongation of the an specified amount of bases

github.com/apeltzer/CircularMapper github.com/apeltzer/CircularMapper/blob/master/docs/contents/userguide.rst https://github.com/apeltzer/CircularMapper no DOI available
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