Groovy Map containing sample information
e.g. [ id:‘test’, single_end
]
fasta:file
Nucleic or amino acid sequence file in FASTA format.
*.{fasta,fna,fa,fasta.gz,fna.gz,fa.gz}
mode:string
The mode to run Busco in. One of genome, proteins, or transcriptome
{genome,proteins,transcriptome}
lineage:string
The BUSCO lineage to use, or “auto”, “auto_prok” or “auto_euk” to automatically select lineage
busco_lineages_path:directory
Path to local BUSCO lineages directory.
config_file:file
Path to BUSCO config file.
Output
name:type
description
pattern
batch_summary
meta:map
Groovy Map containing sample information
e.g. [ id:‘test’ ]
*-busco.batch_summary.txt:file
Summary of all sequence files analyzed
*-busco.batch_summary.txt
short_summaries_txt
meta:map
Groovy Map containing sample information
e.g. [ id:‘test’ ]
short_summary.*.txt:file
Short Busco summary in plain text format
short_summary.*.txt
short_summaries_json
meta:map
Groovy Map containing sample information
e.g. [ id:‘test’ ]
short_summary.*.json:file
Short Busco summary in JSON format
short_summary.*.json
full_table
meta:map
Groovy Map containing sample information
e.g. [ id:‘test’ ]
*-busco/*/run_*/full_table.tsv:file
Full BUSCO results table
full_table.tsv
missing_busco_list
meta:map
Groovy Map containing sample information
e.g. [ id:‘test’ ]
*-busco/*/run_*/missing_busco_list.tsv:file
List of missing BUSCOs
missing_busco_list.tsv
single_copy_proteins
meta:map
Groovy Map containing sample information
e.g. [ id:‘test’ ]
*-busco/*/run_*/single_copy_proteins.faa:file
Fasta file of single copy proteins (transcriptome mode)
single_copy_proteins.faa
seq_dir
meta:map
Groovy Map containing sample information
e.g. [ id:‘test’ ]
*-busco/*/run_*/busco_sequences:directory
BUSCO sequence directory
busco_sequences
translated_dir
meta:map
Groovy Map containing sample information
e.g. [ id:‘test’ ]
*-busco/*/translated_proteins:directory
Six frame translations of each transcript made by the transcriptome mode
translated_dir
busco_dir
meta:map
Groovy Map containing sample information
e.g. [ id:‘test’ ]
*-busco:directory
BUSCO lineage specific output
*-busco
downloaded_lineages
meta:map
Groovy Map containing sample information
e.g. [ id:‘test’ ]
busco_downloads/lineages/*:directory
Lineages downloaded by BUSCO when running the analysis, for example bacteria_odb12
busco_downloads/lineages/*
versions
versions.yml:file
File containing software versions
versions.yml
Tools
busco
MIT
BUSCO provides measures for quantitative assessment of genome assembly, gene set, and transcriptome completeness based on evolutionarily informed expectations of gene content from near-universal single-copy orthologs selected from OrthoDB.