panaroo
Tags: pangenome pan-genome comparative-genomics core-genome alignment run-scope
Build a pangenome from GFF3 annotations using Panaroo.
This subworkflow creates a pangenome from bacterial genome annotations using Panaroo. Panaroo is a pangenome pipeline that produces polished pangenomes by removing errors and contamination from input annotations. It generates gene presence/absence matrices and core-genome alignments suitable for downstream phylogenetic analysis.
Take
gff: Channel<Record>
| Field | Description |
|---|---|
meta | Groovy Record containing sample information |
gff | Set of GFF3 annotation files representing the genomic annotations for each sample |
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 |
|---|---|
aln | Core genome alignment in FASTA format (optional) |
filtered_aln | Core genome alignment with recombinant regions filtered out (optional) |
csv | Gene presence/absence matrix in Roary-compatible CSV format (optional) |
panaroo_csv | Gene presence/absence matrix in Panaroo's native CSV format (optional) |
supplemental | Directory containing Panaroo intermediate files and data structures |
Module Composition
This subworkflow calls the following modules:
- panaroo_run - Fast and scalable bacterial pangenome analysis using a graph-based approach.
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) -
Panaroo
Tonkin-Hill G, MacAlasdair N, Ruis C, Weimann A, Horesh G, Lees JA, Gladstone RA, Lo S, Beaudoin C, Floto RA, Frost SDW, Corander J, Bentley SD, Parkhill J Producing polished prokaryotic pangenomes with the Panaroo pipeline. Genome Biology 21(1), 180. (2020)