clonalframeml

Tags: bacteria recombination phylogeny alignment msa evolution run-scope

Inference of recombination in bacterial genomes.

Uses ClonalFrameML to detect recombination events in bacterial genomes. It corrects the phylogenetic tree for recombination and produces a "masked" alignment where recombinant regions are removed, allowing for more accurate phylogenetic inference.

Inputs

record (
    meta: Record,
    aln: Path,
    nwk: Path
)

Field	Type	Description
meta	Record	Groovy Record containing sample information
aln	Path	Multiple sequence alignment in FASTA format
nwk	Path	Initial phylogenetic tree in Newick format

Outputs

record (
    meta: Record,
    emsim: Path?,
    em: Path,
    status: Path,
    nwk: Path,
    fasta: Path,
    pos_ref: Path,
    masked_aln: Path,
    results: Set<Path>,
    logs: Set<Path?>,
    nf_logs: Set<Path>,
    versions: Set<Path>
)

Field	Type	Description
meta	Record	Sample information record
emsim	Path?	Uncertainty estimation results (if requested)
em	Path	Final parameter estimates from the EM algorithm
status	Path	Tab-delimited list of predicted recombination events (importations)
nwk	Path	The input tree with internal nodes labelled
fasta	Path	Reconstructed ancestral sequences (*.fasta.gz)
pos_ref	Path	Position cross-reference table (*.txt.gz)
masked_aln	Path	The input alignment with recombinant regions 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

ClonalFrameML Parameters

Parameter	Type	Default	Description
--clonalframeml_emsim	integer	100	Number of simulations to estimate uncertainty in the EM results
--skip_recombination	boolean	false	Skip ClonalFrameML execution in subworkflows

Used By

Subworkflows

• clonalframeml - Detect and mask recombination events in bacterial phylogenies.

Workflows

• pangenome - Pangenome analysis with optional core-genome phylogeny.

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)

• ClonalFramML
  Didelot X, Wilson DJ ClonalFrameML: Efficient Inference of Recombination in Whole Bacterial Genomes. PLoS Comput Biol 11(2) e1004041 (2015)

• maskrc-svg
  Kwong J maskrc-svg - Masks recombination as detected by ClonalFrameML or Gubbins and draws an SVG. (GitHub)

Source

View source on GitHub

Version

CLONALFRAMEML:
    - clonalframeml: 1.12