Nextflow Registry | nf-core/kmergenie@0.0.0-0c7146d

nf-core/kmergenie @ 0.0.0-0c7146d

KmerGenie estimates the best k-mer length for genome de novo assembly

k-mer count genome assembly

Latest version: 0.0.0-0c7146d

Total downloads: 1

Source: nf-core/modules

Authors: @LiaOb21

Maintainers: @LiaOb21

KmerGenie estimates the best k-mer length for genome de novo assembly

Add the following snippet to your workflow script to include this module.

include { KMERGENIE } from 'nf-core/kmergenie'

MIT License

Process

`Name`	`KMERGENIE`

Input 1 channel

#1 tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`reads` file	Input reads in FastQ format `*.{fastq.gz, fastq, fq.gz, fq}`

Output 6 channels

#1 dat tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.dat` file	text file containing number of kmer for kmer sizes and recommended coverage cut-off `*.dat`

#2 log tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.kmergenie.log` file	log file containing the standard output and error of the kmergenie command `*.kmergenie.log`

#3 pdf tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.pdf` file	histogram plots obtained from individual kmer sizes `*.pdf`

#4 html tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*_report.html` file	html file containing all the plotted histograms obtained from different kmer size `*_report.html`

#5 histo tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.histo` file	histogram files (text) obtained from individual kmer sizes `*.histo`

#6 versions_kmergenie tuple

`${task.process}` string	The name of the process
`kmergenie` string	The name of the tool
`kmergenie --version \|& sed "1!d ; s/KmerGenie //"` eval	The expression to obtain the version of the tool

Tool	Description	Homepage
kmergenie	KmerGenie estimates the best k-mer length for genome de novo assembly. Given a set of reads, KmerGenie first computes the k-mer abundance histogram for many values of k. Then, for each value of k, it predicts the number of distinct genomic k-mers in the dataset, and returns the k-mer length which maximizes this number.	http://kmergenie.bx.psu.edu/

Version	0.0.0-0c7146d
Commit ID	135d883a43b1a2324b4112cd270cf22e20835533
Release Date	08 Apr 2026 18:51:12 (UTC)
Download URL	https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Fkmergenie/0.0.0-0c7146d/download
OCI Store URL	https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/kmergenie/blobs/sha256:09379744a6b4e9ae299e8aebbb66c14b2b3e003b5f11e93b8e58c8eddef2f701
Size	3.4 KB
Checksum	sha256:09379744a6b4e9ae299e8aebbb66c14b2b3e003b5f11e93b8e58c8eddef2f701
Downloads	1

Version	Date	Status	Downloads	Size	Diff
0.0.0-0c7146d	08 Apr 2026 18:51:12 (UTC)		1	3.4 KB	-