Description

Benchmarking Universal Single Copy Orthologs

Input

name:type
description
pattern

meta{:bash}

:map

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

fasta{:bash}

:file

Nucleic or amino acid sequence file in FASTA format.

*.{fasta,fna,fa,fasta.gz,fna.gz,fa.gz}

mode{:bash}

:string

The mode to run Busco in. One of genome, proteins, or transcriptome

{genome,proteins,transcriptome}

lineage{:bash}

:string

The BUSCO lineage to use, or “auto”, “auto_prok” or “auto_euk” to automatically select lineage

busco_lineages_path{:bash}

:directory

Path to local BUSCO lineages directory.

config_file{:bash}

:file

Path to BUSCO config file.

clean_intermediates{:bash}

:boolean

Flag to remove intermediate files.

Output

name:type
description
pattern

batch_summary{:bash}

meta{:bash}

:map

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

*-busco.batch_summary.txt{:bash}

:file

Summary of all sequence files analyzed

*-busco.batch_summary.txt

short_summaries_txt{:bash}

meta{:bash}

:map

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

short_summary.*.txt{:bash}

:file

Short Busco summary in plain text format

short_summary.*.txt

short_summaries_json{:bash}

meta{:bash}

:map

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

short_summary.*.json{:bash}

:file

Short Busco summary in JSON format

short_summary.*.json

log{:bash}

meta{:bash}

:map

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

*-busco.log{:bash}

:file

BUSCO main log

*-busco.log

full_table{:bash}

meta{:bash}

:map

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

*-busco/*/run_*/full_table.tsv{:bash}

:file

Full BUSCO results table

full_table.tsv

missing_busco_list{:bash}

meta{:bash}

:map

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

*-busco/*/run_*/missing_busco_list.tsv{:bash}

:file

List of missing BUSCOs

missing_busco_list.tsv

single_copy_proteins{:bash}

meta{:bash}

:map

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

*-busco/*/run_*/single_copy_proteins.faa{:bash}

:file

Fasta file of single copy proteins (transcriptome mode)

single_copy_proteins.faa

seq_dir{:bash}

meta{:bash}

:map

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

*-busco/*/run_*/busco_sequences{:bash}

:directory

BUSCO sequence directory

busco_sequences

translated_dir{:bash}

meta{:bash}

:map

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

*-busco/*/translated_proteins{:bash}

:directory

Six frame translations of each transcript made by the transcriptome mode

translated_dir

busco_dir{:bash}

meta{:bash}

:map

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

*-busco{:bash}

:directory

BUSCO lineage specific output

*-busco

downloaded_lineages{:bash}

meta{:bash}

:map

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

busco_downloads/lineages/*{:bash}

:directory

Lineages downloaded by BUSCO when running the analysis, for example bacteria_odb12

busco_downloads/lineages/*

single_copy_faa{:bash}

meta{:bash}

:map

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

*-busco/*/run_*/busco_sequences/single_copy_busco_sequences/*.faa{:bash}

:file

Single copy .faa sequence files

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

single_copy_fna{:bash}

meta{:bash}

:map

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

*-busco/*/run_*/busco_sequences/single_copy_busco_sequences/*.fna{:bash}

:file

Single copy .fna sequence files

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

versions{:bash}

versions.yml{:bash}

: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
bacassdenovotranscriptgenomeassemblergenomeqcmagpathogensurveillance
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
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