gubbins

Tags: bacteria recombination phylogeny alignment msa evolution snp run-scope

Detect recombination and construct a recombination-free phylogeny.

Uses Gubbins (Genealogies Unbiased By recomBinations In Nucleotide Sequences) to iteratively identify and mask recombinant regions in a multiple sequence alignment. It generates a phylogenetic tree based only on vertically inherited point mutations.

Inputs

record (
    meta: Record,
    aln: Path
)

Field	Type	Description
meta	Record	Groovy Record containing sample information
aln	Path	Multiple sequence alignment in FASTA format

Outputs

record (
    meta: Record,
    masked_aln: Path,
    results: Set<Path>,
    logs: Set<Path?>,
    nf_logs: Set<Path>,
    versions: Set<Path>
)

Field	Type	Description
meta	Record	Sample information record
masked_aln	Path	The input alignment with recombinant regions masked (*.masked.aln.gz)
results	Set<Path>	All output files to be published
logs	Set<Path?>	Optional program specific log files
nf_logs	Set<Path>	Nextflow-specific log files (e.g. .command.{begin
versions	Set<Path>	A YAML formatted file with program versions

Parameters

Gubbins Parameters

Parameter	Type	Default	Description
--gubbins_iterations	integer	5	Maximum number of iterations
--gubbins_opts	string		Extra Gubbins options in quotes
--skip_recombination	boolean	false	Skip Gubbins execution in subworkflows

Used By

Subworkflows

• gubbins - Detect and filter recombination regions in bacterial alignments.

Workflows

• snippy - Rapid haplotype variant calling and core genome alignment.

Citations

If you use this in your analysis, please cite the following.

• Bactopia
  Petit III RA, Read TD Bactopia - a flexible pipeline for complete analysis of bacterial genomes. mSystems 5 (2020)

• Gubbins
  Croucher NJ, Page AJ, Connor TR, Delaney AJ, Keane JA, Bentley SD, Parkhill J, Harris SR Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins. Nucleic Acids Research 43(3), e15. (2015)

Source

View source on GitHub

Version

GUBBINS:
    - gubbins: 3.4.3