modules/gubbins

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.

recombinationalignmentphylogeny

https://github.com/nf-core/modules/[...]/modules/nf-core/gubbins

Description

Input

name:type

description

pattern

`alignment:file`

fasta alignment file

*.{fasta,fas,fa,aln}

Output

name:type

description

pattern

`fasta`

`*.fasta:file`

Filtered variant alignment in fasta format

*.{fasta}

`gff`

`*.gff:file`

Recombination predictions in gff format

*.{gff}

`vcf`

`*.vcf:file`

SNP distribution

*.{vcf}

`stats`

`*.csv:file`

Per branch statistics

*.{csv}

`phylip`

`*.phylip:file`

Filtered variant alignment in phylip format

*.{phylip}

`embl_predicted`

`*.recombination_predictions.embl:file`

Recombination predictions in embl format

*.{recombination_predictions.embl}

`embl_branch`

`*.branch_base_reconstruction.embl:file`

Branch base reconstruction

*.{branch_base_reconstruction.embl}

`tree`

`*.final_tree.tre:file`

Recombination removed RAxML phylogenetic tree

*.{final_tree.tre}

`tree_labelled`

`*.node_labelled.final_tree.tre:file`

Recombination removed RAxML phylogenetic tree (nodes labelled)

*.{node_labelled.final_tree.tre}

`versions`

`versions.yml:file`

File containing software versions

versions.yml

Tools

gubbins

Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins.

sanger-pathogens.github.io/gubbins