Description

Benchmarking Universal Single Copy Orthologs

Input

Name
Description
Pattern

meta (map)

Groovy Map containing sample information e.g. [ id:'test', single_end:false ]

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.

clean_intermediates (boolean)

Flag to remove intermediate files.

Output

Name
Description
Pattern

log

meta (map)

Groovy Map containing sample information e.g. [ id:'test' ]

*-busco.log (file)

BUSCO main log

*-busco.log

seq_dir

meta (map)

Groovy Map containing sample information e.g. [ id:'test' ]

*-busco/*/run_*/busco_sequences (directory)

BUSCO sequence directory

busco_sequences

busco_dir

meta (map)

Groovy Map containing sample information e.g. [ id:'test' ]

*-busco (directory)

BUSCO lineage specific output

*-busco

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

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

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

versions_busco

${task.process} (string)

The name of the process

busco (string)

The name of the tool

busco --version 2> /dev/null | sed 's/BUSCO //g' (eval)

The expression to obtain the version of the tool

single_copy_faa

meta (map)

Groovy Map containing sample information e.g. [ id:'test' ]

*-busco/*/run_*/busco_sequences/single_copy_busco_sequences/*.faa (file)

Single copy .faa sequence files

*-busco/*/run_*/busco_sequences/single_copy_busco_sequences/*.faa

single_copy_fna

meta (map)

Groovy Map containing sample information e.g. [ id:'test' ]

*-busco/*/run_*/busco_sequences/single_copy_busco_sequences/*.fna (file)

Single copy .fna sequence files

*-busco/*/run_*/busco_sequences/single_copy_busco_sequences/*.fna

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

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/*

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

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

restructure_busco_output

meta (map)

Groovy Map containing sample information e.g. [ id:'test' ]

lineage (string)

The lineage of the BUSCO gene set

*-busco.batch_summary.txt (file)

Summary of all sequence files analyzed

*-busco.batch_summary.txt

short_summary.*.txt (file)

Short Busco summary in plain text format

short_summary.*.txt

short_summary.*.json (file)

Short Busco summary in JSON format

short_summary.*.json

*-busco/*/run_*/full_table.tsv (file)

Full BUSCO results table

full_table.tsv

*-busco/*/run_*/missing_busco_list.tsv (file)

List of missing BUSCOs

missing_busco_list.tsv

*-busco/*/run_*/busco_sequences (directory)

BUSCO sequence directory

busco_sequences

Topics

Name
Description
Pattern

versions

${task.process} (string)

The name of the process

busco (string)

The name of the tool

busco --version 2> /dev/null | sed 's/BUSCO //g' (eval)

The expression to obtain the version of the tool

Tools

busco Documentation

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.

https://gitlab.com/ezlab/buscodoi: 10.1007/978-1-4939-9173-0_14License: MIT
Pipelines with this module
busco
Authors