---
name: "busco"
section: "1"
platform: "linux"
package: "busco"
version: "5.5.0-3"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/busco"
---

# busco(1)

benchmarking sets of universal single-copy orthologs

## NAME

busco - benchmarking sets of universal single-copy orthologs

## DESCRIPTION

usage: busco **-i** \[SEQUENCE\_FILE\] **-l** \[LINEAGE\] **-o** \[OUTPUT\_NAME\] **-m** \[MODE\] \[OTHER OPTIONS\]

Welcome to BUSCO 5.2.2: the Benchmarking Universal Single-Copy Ortholog assessment tool. For more detailed usage information, please review the README file provided with this distribution and the BUSCO user guide. Visit this page https://gitlab.com/ezlab/busco#how-to-cite-busco to see how to cite BUSCO

### optional arguments:

- **-i** SEQUENCE\_FILE, **--in** SEQUENCE\_FILE

  Input sequence file in FASTA format. Can be an assembled genome or transcriptome (DNA), or protein sequences from an annotated gene set. Also possible to use a path to a directory containing multiple input files.

- **-o** OUTPUT, **--out** OUTPUT

  Give your analysis run a recognisable short name. Output folders and files will be labelled with this name. WARNING: do not provide a path

- **-m** MODE, **--mode** MODE

  Specify which BUSCO analysis mode to run. There are three valid modes: - geno or genome, for genome assemblies (DNA) - tran or transcriptome, for transcriptome assemblies (DNA) - prot or proteins, for annotated gene sets (protein)

- **-l** LINEAGE, **--lineage\_dataset** LINEAGE

  Specify the name of the BUSCO lineage to be used.

- **--augustus**

  Use augustus gene predictor for eukaryote runs

- **--augustus\_parameters** "--PARAM1=VALUE1,--PARAM2=VALUE2"

  Pass additional arguments to Augustus. All arguments should be contained within a single pair of quotation marks, separated by commas.

- **--augustus\_species** AUGUSTUS\_SPECIES

  Specify a species for Augustus training.

- **--auto-lineage**

  Run auto-lineage to find optimum lineage path

- **--auto-lineage-euk**

  Run auto-placement just on eukaryote tree to find optimum lineage path

- **--auto-lineage-prok**

  Run auto-lineage just on non-eukaryote trees to find optimum lineage path

- **-c** N, **--cpu** N

  Specify the number (N=integer) of threads/cores to use.

- **--config** CONFIG\_FILE

  Provide a config file

- **--datasets\_version** DATASETS\_VERSION

  Specify the version of BUSCO datasets, e.g. odb10

- **--download** \[dataset ...\]

  Download dataset. Possible values are a specific dataset name, "all", "prokaryota", "eukaryota", or "virus". If used together with other command line arguments, make sure to place this last.

- **--download\_base\_url** DOWNLOAD\_BASE\_URL

  Set the url to the remote BUSCO dataset location

- **--download\_path** DOWNLOAD\_PATH

  Specify local filepath for storing BUSCO dataset downloads

- **-e** N, **--evalue** N

  E-value cutoff for BLAST searches. Allowed formats, 0.001 or 1e-03 (Default: 1e-03)

- **-f**, **--force**

  Force rewriting of existing files. Must be used when output files with the provided name already exist.

- **-h**, **--help**

  Show this help message and exit

- **--limit** N

  How many candidate regions (contig or transcript) to consider per BUSCO (default: 3)

- **--list-datasets**

  Print the list of available BUSCO datasets

- **--long**

  Optimization Augustus self-training mode (Default: Off); adds considerably to the run time, but can improve results for some non-model organisms

- **--metaeuk\_parameters** "--PARAM1=VALUE1,--PARAM2=VALUE2"

  Pass additional arguments to Metaeuk for the first run. All arguments should be contained within a single pair of quotation marks, separated by commas.

- **--metaeuk\_rerun\_parameters** "--PARAM1=VALUE1,--PARAM2=VALUE2"

  Pass additional arguments to Metaeuk for the second run. All arguments should be contained within a single pair of quotation marks, separated by commas.

- **--offline**

  To indicate that BUSCO cannot attempt to download files

- **--out\_path** OUTPUT\_PATH

  Optional location for results folder, excluding results folder name. Default is current working directory.

- **-q**, **--quiet**

  Disable the info logs, displays only errors

- **-r**, **--restart**

  Continue a run that had already partially completed.

- **--tar**

  Compress some subdirectories with many files to save space

- **--update-data**

  Download and replace with last versions all lineages datasets and files necessary to their automated selection

- **-v**, **--version**

  Show this version and exit

## AUTHOR

 This manpage was written by Nilesh Patra for the Debian distribution and\
  can be used for any other usage of the program.