Description

Perl script (generateMap.pl) generates the mappability of a genome given a certain size of reads, for input to hmmcopy mapcounter. Takes a very long time on large genomes, is not parallelised at all.

Input

name:type
description
pattern

meta{:bash}

:map

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

fasta{:bash}

:file

Input genome fasta file

Output

name:type
description
pattern

bigwig{:bash}

meta{:bash}

:map

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

*.bw{:bash}

:file

bigwig file containing the mappability of the genome

*.bw

versions_hmmcopy{:bash}

${task.process}{:bash}

:string

The name of the process

hmmcopy{:bash}

:string

The name of the tool

0.1.1{:bash}

:string

The expression to obtain the version of the tool

Topics

name:type
description
pattern

versions{:bash}

${task.process}{:bash}

:string

The name of the process

hmmcopy{:bash}

:string

The name of the tool

0.1.1{:bash}

:string

The expression to obtain the version of the tool

Tools

hmmcopy
GPL v3

C++ based programs for analyzing BAM files and preparing read counts -- used with bioconductor-hmmcopy

github.com/shahcompbio/hmmcopy_utils
maintainers
Github user sppearce
Github user adamrtalbot
get in touch
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