Description

masks sequences in a FASTA file based on intervals defined in a feature file.

Input

Name (Type)
Description
Pattern

meta (map)

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

]

bed (file)

Bed feature file

*.{bed}

fasta (file)

Input fasta file

*.{fa,fasta}

Output

Name (Type)
Description
Pattern

meta (map)

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

]

fasta (file)

Output masked fasta file

*.{fa}

versions (file)

File containing software versions

versions.yml
included in
callingcards viralrecon
authors
Github user joseespinosa Github user drpatelh
get in touch
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Tools

bedtools
MIT

A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types.

bedtools.readthedocs.io/en/latest/content/tools/intersect