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_gubbins`

`${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

Topics

name:type

description

pattern

`versions`

`${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

Tools

gubbins

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

sanger-pathogens.github.io/gubbins

modules/gubbins

Description

Input

`alignment`
`:file`

Output

`fasta`

`*.fasta`
`:file`

`gff`

`*.gff`
`:file`

`vcf`

`*.vcf`
`:file`

`stats`

`*.csv`
`:file`

`phylip`

`*.phylip`
`:file`

`embl_predicted`

`*.recombination_predictions.embl`
`:file`

`embl_branch`

`*.branch_base_reconstruction.embl`
`:file`

`tree`

`*.final_tree.tre`
`:file`

`tree_labelled`

`*.node_labelled.final_tree.tre`
`:file`

`versions_gubbins`

`${task.process}`
`:string`

`gubbins`
`:string`

`run_gubbins.py --version 2>&1`
`:eval`

Topics

`versions`

`${task.process}`
`:string`

`gubbins`
`:string`

`run_gubbins.py --version 2>&1`
`:eval`

Tools

gubbins

maintainer

get in touch

modules/gubbins

Description

Input

alignment:file

Output

fasta

*.fasta:file

gff

*.gff:file

vcf

*.vcf:file

stats

*.csv:file

phylip

*.phylip:file

embl_predicted

*.recombination_predictions.embl:file

embl_branch

*.branch_base_reconstruction.embl:file

tree

*.final_tree.tre:file

tree_labelled

*.node_labelled.final_tree.tre:file

versions_gubbins

${task.process}:string

gubbins:string

run_gubbins.py --version 2>&1:eval

Topics

versions

${task.process}:string

gubbins:string

run_gubbins.py --version 2>&1:eval

Tools

gubbins

maintainer

get in touch

`alignment`
`:file`

`fasta`

`*.fasta`
`:file`

`gff`

`*.gff`
`:file`

`vcf`

`*.vcf`
`:file`

`stats`

`*.csv`
`:file`

`phylip`

`*.phylip`
`:file`

`embl_predicted`

`*.recombination_predictions.embl`
`:file`

`embl_branch`

`*.branch_base_reconstruction.embl`
`:file`

`tree`

`*.final_tree.tre`
`:file`

`tree_labelled`

`*.node_labelled.final_tree.tre`
`:file`

`versions_gubbins`

`${task.process}`
`:string`

`gubbins`
`:string`

`run_gubbins.py --version 2>&1`
`:eval`

`versions`

`${task.process}`
`:string`

`gubbins`
`:string`

`run_gubbins.py --version 2>&1`
`:eval`