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:map

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

fasta:file

Input genome fasta file

Output

name:type
description
pattern

bigwig

meta:map

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

*.bw:file

bigwig file containing the mappability of the genome

*.bw

versions

versions.yml:file

File containing software versions

versions.yml

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
Ask a question on Slack Open an issue on GitHub