busco

Tags: quality-control completeness genome assembly orthologs busco sample-scope

Assess genome assembly completeness using single-copy orthologs.

Uses BUSCO (Benchmarking Universal Single-Copy Orthologs) to measure the completeness of genome assemblies, gene sets, or transcriptomes by matching them against a lineage-specific set of conserved orthologs.

Inputs

record (
    meta: Record,
    fna: Path
)

Field	Type	Description
meta	Record	Groovy Record containing sample information
fna	Path	Assembled contigs in FASTA format

Outputs

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

Field	Type	Description
meta	Record	Sample information record
tsv	Path	Text summary report of the completeness score (C/S/D/F/M%)
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

BUSCO Parameters

Parameter	Type	Default	Description
--busco_lineage	string	bacteria_odb10	Specify the name of the BUSCO lineage to be used
--busco_evalue	string	1e-03	E-value cutoff for BLAST searches. Allowed formats, 0.001 or 1e-03
--busco_limit	integer	3	Total candidate regions to consider per BUSCO

Used By

Subworkflows

• busco - Assess genome assembly completeness using BUSCO.

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)

Source

View source on GitHub

Version

BUSCO:
    - busco: 6.0.0