Description

Dumps the results from a jellyfish binary file into a human readable format

Input

name:type
description
pattern

meta{:bash}

:map

Groovy Map containing sample information e.g. [ id:'sample1' ]

jf{:bash}

:file

Jellyfish binary k-mer database

*.jf

Output

name:type
description
pattern

output{:bash}

meta{:bash}

:map

Groovy Map containing sample information e.g. [ id:'sample1' ]

${prefix}.${extension}{:bash}

:file

Human readable k-mer database in fasta format, or in 2-column space delimited format if the -c argument is provided

*.{fa,txt}

versions{:bash}

versions.yml{:bash}

:file

File containing software versions

versions.yml

Tools

jellyfish
GPL v3

Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA. A k-mer is a substring of length k, and counting the occurrences of all such substrings is a central step in many analyses of DNA sequence

github.com/gmarcais/Jellyfish github.com/gmarcais/Jellyfish/blob/master/doc/Readme.md https://github.com/gmarcais/Jellyfish 10.1093/bioinformatics/btr011
maintainer
Github user vagkaratzas
get in touch
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