Description

Benchmarking Universal Single Copy Orthologs

Input

Name (Type)
Description
Pattern

meta (map)

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” 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

meta (map)

Groovy Map containing sample information
e.g. [ id:‘test’, single_end

]

batch_summary (file)

Summary of all sequence files analyzed

*-busco.batch_summary.txt

short_summaries_txt (file)

Short Busco summary in plain text format

short_summary.*.txt

short_summaries_json (file)

Short Busco summary in JSON format

short_summary.*.json

busco_dir (directory)

BUSCO lineage specific output

*-busco

full_table (file)

Full BUSCO results table

full_table.tsv

missing_busco_list (file)

List of missing BUSCOs

missing_busco_list.tsv

single_copy_proteins (file)

Fasta file of single copy proteins (transcriptome mode)

single_copy_proteins.faa

seq_dir (directory)

BUSCO sequence directory

busco_sequences

translated_dir (directory)

Six frame translations of each transcript made by the transcriptome mode

translated_dir

versions (file)

File containing software versions

versions.yml
included in
denovotranscript
maintainers
Github user priyanka-surana
Github user charles-plessy
Github user mahesh-panchal
Github user muffato
Github user jvhagey
Github user gallvp
get in touch
Ask a question on Slack Open an issue on GitHub

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.

busco.ezlab.org busco.ezlab.org/busco_userguide https://gitlab.com/ezlab/busco 10.1007/978-1-4939-9173-0_14