modules/busco

Benchmarking Universal Single Copy Orthologs

quality controlgenometranscriptomeproteome

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

]

`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_proteins:directory`

Six frame translations of each transcript made by the transcriptome mode

translated_proteins

`versions: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

included in

maintainers

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Ask a question on Slack Open an issue on GitHub

modules/busco

Description

Input

meta:map

fasta:file

mode:string

lineage:string

busco_lineages_path:directory

config_file:file

Output

meta:map

batch_summary:file

short_summaries_txt:file

short_summaries_json:file

busco_dir:directory

full_table:file

missing_busco_list:file

single_copy_proteins:file

seq_dir:directory

translated_proteins:directory

versions:file

Tools

busco MIT

included in

maintainers

get in touch

`meta:map`

`fasta:file`

`mode:string`

`lineage:string`

`busco_lineages_path:directory`

`config_file:file`

`meta:map`

`batch_summary:file`

`short_summaries_txt:file`

`short_summaries_json:file`

`busco_dir:directory`

`full_table:file`

`missing_busco_list:file`

`single_copy_proteins:file`

`seq_dir:directory`

`translated_proteins:directory`

`versions:file`

busco
MIT