Description

Efficiently counts k-mers from DNA sequencing reads using a fast, memory-efficient, parallelized algorithm

Input

name:type
description
pattern

meta{:bash}

:map

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

fasta{:bash}

:file

Nucleotide sequences in FASTA format

*.{fasta,fa,fna,faa}

kmer_length{:bash}

:integer

k-mer size to use

size{:bash}

:string

Specifies the memory hash size (in bytes) to allocate for the k-mer counting hash table (e.g., ‘100M’). A mean estimation could be carried with this formula: ‘genome size + (genome size * coverage * kmer-length * error rate)’

Output

name:type
description
pattern

jf{:bash}

meta{:bash}

:map

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

${prefix}.jf{:bash}

:file

Jellyfish binary k-mer database

*.jf

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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