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

]

`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’, single_end

]

`*-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’, single_end

]

`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’, single_end

]

`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’, single_end

]

`-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’, single_end

]

`-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’, single_end

]

`-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’, single_end

]

`-busco//run_*/busco_sequences:directory`

BUSCO sequence directory

busco_sequences

`translated_dir`

`meta:map`

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

]

`-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’, single_end

]

`*-busco:directory`

BUSCO lineage specific output

*-busco

`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

modules/busco_busco

Description

Input

meta:map

fasta:file

mode:string

lineage:string

busco_lineages_path:directory

config_file:file

Output

batch_summary

meta:map

*-busco.batch_summary.txt:file

short_summaries_txt

meta:map

short_summary.*.txt:file

short_summaries_json

meta:map

short_summary.*.json:file

full_table

meta:map

*-busco/*/run_*/full_table.tsv:file

missing_busco_list

meta:map

*-busco/*/run_*/missing_busco_list.tsv:file

single_copy_proteins

meta:map

*-busco/*/run_*/single_copy_proteins.faa:file

seq_dir

meta:map

*-busco/*/run_*/busco_sequences:directory

translated_dir

meta:map

*-busco/*/translated_proteins:directory

busco_dir

meta:map

*-busco:directory

versions

versions.yml: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`

`batch_summary`

`meta:map`

`*-busco.batch_summary.txt:file`

`short_summaries_txt`

`meta:map`

`short_summary.*.txt:file`

`short_summaries_json`

`meta:map`

`short_summary.*.json:file`

`full_table`

`meta:map`

`-busco//run_*/full_table.tsv:file`

`missing_busco_list`

`meta:map`

`-busco//run_*/missing_busco_list.tsv:file`

`single_copy_proteins`

`meta:map`

`-busco//run_*/single_copy_proteins.faa:file`

`seq_dir`

`meta:map`

`-busco//run_*/busco_sequences:directory`

`translated_dir`

`meta:map`

`-busco//translated_proteins:directory`

`busco_dir`

`meta:map`

`*-busco:directory`

`versions`

`versions.yml:file`

busco
MIT