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

]

fasta (file)

Input genome fasta file

Output

Name (Type)
Description
Pattern

meta (map)

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

]

versions (file)

File containing software versions

versions.yml

bigwig (file)

bigwig file containing the mappability of the genome

*.bw
maintainers
Github user sppearce
Github user adamrtalbot
get in touch
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Tools

hmmcopy
GPL v3

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

github.com/shahcompbio/hmmcopy_utils