nf-core/jellyfish/count @ 0.0.0-3fc6d40
Summary
Efficiently counts k-mers from DNA sequencing reads using a fast, memory-efficient, parallelized algorithm
Get started
Add the following snippet to your workflow script to include this module.
include { JELLYFISH_COUNT } from 'nf-core/jellyfish/count'
License
MIT License
Process
Name
|
JELLYFISH_COUNT |
|---|
Input
3 channels
#1
tuple
meta
map
|
Groovy Map containing sample information e.g. |
|---|---|
fasta
file
|
Nucleotide sequences in FASTA format *.{fasta,fa,fna,faa}
|
kmer_length
integer
|
k-mer size to use |
|---|
size
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
2 channels
#1
jf
tuple
meta
map
|
Groovy Map containing sample information e.g. |
|---|---|
${prefix}.jf
file
|
Jellyfish binary k-mer database *.jf
|
#2
versions
versions.yml
file
|
File containing software versions versions.yml
|
|---|
| Tool | Description | Homepage |
|---|---|---|
| jellyfish | 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 | https://github.com/gmarcais/Jellyfish |
| Version | 0.0.0-3fc6d40 |
|---|---|
| Commit ID | 6c4ed3a220310b905a1fc9d04f05be2e0837142b |
| Release Date | 22 Apr 2026 15:18:19 (UTC) |
| Download URL | https://registry.nextflow.io/api/v1/modules/nf-core%2Fjellyfish%2Fcount/0.0.0-3fc6d40/download |
| OCI Store URL | https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/jellyfish/count/blobs/sha256:0613d8e84f40e51b7452dff69779b73707e414da81fa53958430b508263fbde2 |
| Size | 2.5 KB |
| Checksum | sha256:0613d8e84f40e51b7452dff69779b73707e414da81fa53958430b508263fbde2 |
| Downloads | 3 |
| Version | Date | Status | Downloads | Size |
|---|---|---|---|---|
| 0.0.0-6c4ed3a | 23 Apr 2026 15:26:17 (UTC) | 3 | 2.5 KB | |
| 0.0.0-3fc6d40 | 22 Apr 2026 15:18:19 (UTC) | 3 | 2.5 KB | |
| 0.0.0-0c7146d | 08 Apr 2026 19:12:05 (UTC) | 3 | 2.5 KB |