Description

Realign reads mapped with BWA to elongated reference genome

Input

name:type
description
pattern

meta{:bash}

:map

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

bam{:bash}

:file

BAM/SAM file

*.{bam,sam}

meta2{:bash}

:map

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

fasta{:bash}

:file

Input elongated genome fasta

meta3{:bash}

:map

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

elongation_factor{:bash}

: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

meta4{:bash}

:map

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

elongated_chr_list{:bash}

:file

File listing the chromosomes that were elongated

*_elongated

Output

name:type
description
pattern

bam{:bash}

meta{:bash}

:map

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

*_realigned.bam{:bash}

:file

Realigned BAM file

*.bam

versions{:bash}

versions.yml{:bash}

:file

File containing software versions

versions.yml

Tools

circularmapper
GPL v3

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

circularmapper.readthedocs.io/en/latest https://github.com/apeltzer/CircularMapper/ 10.1186/s13059-016-0918-z
maintainers
Github user shyama-mama
Github user jbv2
Github user TCLamnidis
get in touch
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