modules/busco_busco

Benchmarking Universal Single Copy Orthologs

quality controlgenometranscriptomeproteome

https://github.com/nf-core/modules/[...]/modules/nf-core/busco/busco

Description

Benchmarking Universal Single Copy Orthologs

Input

name:type

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: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

`log`

`meta`
`:map`

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

`*-busco.log`
`:file`

BUSCO main log

*-busco.log

`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/*

`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

`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.

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