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nf-core/gubbins @ 0.0.0-3fc6d40

Gubbins (Genealogies Unbiased By recomBinations In Nucleotide Sequences) is an algorithm that iteratively identifies loci containing elevated densities of base substitutions while concurrently constructing a phylogeny based on the putative point mutations outside of these regions.

recombination alignment phylogeny
Latest version: 0.0.0-6c4ed3a
Total downloads: 10
Source: nf-core/modules
Authors: @avantonder
Maintainers: @avantonder

Summary

Gubbins (Genealogies Unbiased By recomBinations In Nucleotide Sequences) is an algorithm that iteratively identifies loci containing elevated densities of base substitutions while concurrently constructing a phylogeny based on the putative point mutations outside of these regions.

Get started

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

include { GUBBINS } from 'nf-core/gubbins'

License

MIT License

Process
Name GUBBINS
Input 1 channel
alignment file

fasta alignment file

 *.{fasta,fas,fa,aln}
Output 10 channels
#1 gff
*.gff file

Recombination predictions in gff format

 *.{gff}
#2 vcf
*.vcf file

SNP distribution

 *.{vcf}
#3 tree
*.final_tree.tre file

Recombination removed RAxML phylogenetic tree

 *.{final_tree.tre}
#4 fasta
*.fasta file

Filtered variant alignment in fasta format

 *.{fasta}
#5 stats
*.csv file

Per branch statistics

 *.{csv}
#6 phylip
*.phylip file

Filtered variant alignment in phylip format

 *.{phylip}
#7 embl_branch
*.branch_base_reconstruction.embl file

Branch base reconstruction

 *.{branch_base_reconstruction.embl}
#8 tree_labelled
*.node_labelled.final_tree.tre file

Recombination removed RAxML phylogenetic tree (nodes labelled)

 *.{node_labelled.final_tree.tre}
#9 embl_predicted
*.recombination_predictions.embl file

Recombination predictions in embl format

 *.{recombination_predictions.embl}
#10 versions_gubbins tuple
${task.process} string

The name of the process
gubbins string

The name of the tool
run_gubbins.py --version 2>&1 eval

The expression to obtain the version of the tool
Tool Description Homepage
gubbins Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins. https://sanger-pathogens.github.io/gubbins/
Version 0.0.0-3fc6d40
Commit ID 6c4ed3a220310b905a1fc9d04f05be2e0837142b
Release Date 22 Apr 2026 15:15:46 (UTC)
Download URL https://registry.nextflow.io/api/v1/modules/nf-core%2Fgubbins/0.0.0-3fc6d40/download
OCI Store URL https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/gubbins/blobs/sha256:a4685bd956c6b13e7cf592ba6e9b3e42fc8921a07b99b375017f49ae2bac94a1
Size 3.1 KB
Checksum sha256:a4685bd956c6b13e7cf592ba6e9b3e42fc8921a07b99b375017f49ae2bac94a1
Downloads 3
Version Date Status Downloads Size
0.0.0-6c4ed3a 23 Apr 2026 15:23:11 (UTC) 4 3.0 KB
0.0.0-3fc6d40 22 Apr 2026 15:15:46 (UTC) 3 3.1 KB
0.0.0-0c7146d 08 Apr 2026 19:07:25 (UTC) 3