Description

Realign reads mapped with BWA to elongated reference genome

Input

Name (Type)
Description
Pattern

meta (map)

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

bam (file)

BAM/SAM file

*.{bam,sam}

meta2 (map)

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

fasta (file)

Input elongated genome fasta

elongation_factor (integer)

The elongation factor used when running circulargenerator, i.e. the number of bases that the ends of the target chromosome in the reference genome was elongated by

Output

Name (Type)
Description
Pattern

meta (map)

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

bam (file)

Realigned BAM file

*.bam

versions (file)

File containing software versions

versions.yml

Tools

circularmapper
GPL v3

A method to improve mappings on circular genomes such as Mitochondria.