busco
Tags: assembly completeness quality assessment orthologs evaluation sample-scope
Assess genome assembly completeness using BUSCO.
This subworkflow evaluates genome assembly completeness by searching for single-copy orthologs against the BUSCO database. It generates comprehensive completeness reports including missing, duplicated, fragmented, and complete single-copy orthologs. The workflow includes individual sample assessments and a merged summary report across all samples.
Take
assembly: Channel<Record>
| Field | Description |
|---|---|
meta | Groovy Record containing sample information |
assembly | Genome assemblies to evaluate for completeness. Each record contains metadata |
busco_lineage: String
| Name | Type | Description |
|---|---|---|
busco_lineage | String | BUSCO lineage dataset to use for assessment (e.g., bacteria_odb10). |
Emit
Published
The sample_outputs and run_outputs emissions are aggregates of output files that will be published in the entry workflow.
sample_outputs
| Output | Description |
|---|---|
tsv | A text summary report of the completeness score (C/S/D/F/M%) |
supplemental | Directory containing full tables, missing gene lists, and lineage data |
run_outputs
| Output | Description |
|---|---|
csv | Aggregated results in CSV format |
Module Composition
This subworkflow calls the following modules:
- csvtk_concat - Concatenate multiple CSV or TSV files into a single table.
- busco - Assess genome assembly completeness using single-copy orthologs.
Used By
This subworkflow is used by the following workflows:
- busco - Assessment of genome assembly completeness using evolutionarily informed expectations.
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) -
BUSCO
Manni M, Berkeley MR, Seppey M, Simão FA, Zdobnov EM BUSCO Update: Novel and Streamlined Workflows along with Broader and Deeper Phylogenetic Coverage for Scoring of Eukaryotic, Prokaryotic, and Viral Genomes. Molecular Biology and Evolution 38(10), 4647-4654. (2021)