clonalframeml
Tags: recombination phylogeny masking clonalframe bacterial-evolution run-scope
Detect and mask recombination events in bacterial phylogenies.
This subworkflow uses ClonalFrameML to detect and mask recombination events in bacterial phylogenies. It first builds a quick phylogenetic tree using IQ-TREE, then identifies recombination regions and creates a recombination-masked alignment. Finally, it calculates SNP distances from the masked alignment using snp-dists.
Take
alignment: Channel<Record>
| Field | Description |
|---|---|
meta | Groovy Record containing sample information |
aln | Core-genome alignment in FASTA format |
Emit
Published
The sample_outputs and run_outputs emissions are aggregates of output files that will be published in the entry workflow.
sample_outputs
No sample-scope outputs.
run_outputs
| Output | Description |
|---|---|
masked_aln | Recombination-masked alignment with detected recombination regions removed |
emsim | Uncertainty estimation results |
em | Final parameter estimates from the EM algorithm |
status | Predicted recombination events (importations) |
nwk | Input tree with internal nodes labelled |
fasta | Reconstructed ancestral sequences |
pos_ref | Position cross-reference table |
aln | Input multiple sequence alignment (passed through from IQ-TREE) |
nwk | Quick-start maximum-likelihood phylogenetic tree from IQ-TREE |
tsv | Pairwise SNP distances from masked alignment in TSV format |
Downstream Inputs
The following emissions are meant to be used as inputs to downstream subworkflows.
alignment
| Output | Description |
|---|---|
aln | Recombination-masked alignment for downstream phylogenetic analysis |
Subworkflow Composition
This subworkflow calls the following subworkflows:
- iqtree - Construct maximum likelihood phylogenetic trees from alignments.
- snpdists - Calculate pairwise SNP distances from sequence alignments.
Module Composition
This subworkflow calls the following modules:
- clonalframeml - Inference of recombination in bacterial genomes.
Used By
This subworkflow is used by the following 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) -
IQ-TREE
Nguyen L-T, Schmidt HA, von Haeseler A, Minh BQ IQ-TREE: A fast and effective stochastic algorithm for estimating maximum likelihood phylogenies. Mol. Biol. Evol. 32:268-274 (2015) -
snp-dists
Seemann T snp-dists - Pairwise SNP distance matrix from a FASTA sequence alignment. (GitHub)