Description

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

Input

Name (Type)
Description
Pattern

meta (map)

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

reference (file)

Genome fasta file

*.fasta

meta2 (map)

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

elongation_factor (integer)

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

meta3 (map)

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

target (string)

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

Output

Name (Type)
Description
Pattern

meta (map)

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

versions (file)

File containing software versions

versions.yml

fasta (file)

Genome fasta file

*.fasta

elongated (file)

File listing the chromosomes that were elongated

*_elongated
maintainer
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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