BUSCO(1)

💖 NAME 💖

busco — benchmarking sets of universal single-copy orthologs. that's the whole name, she's short and she knows it 💅

✨ DESCRIPTION ✨

okay so bestie, first thing, here's how you actually call her:

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. she's iconic, she's thorough, she checks your genome/transcriptome/protein set and tells you how it's doing. for the deeper usage tea, go read the README file that ships with this distribution and the BUSCO user guide, fr fr.

and if you wanna know how to cite BUSCO (bestie, you GOTTA cite), visit this page: https://gitlab.com/ezlab/busco#how-to-cite-busco 🌸

🦋 optional arguments 🦋

aka the whole menu. every single one, no skipping, periodt.

• -i SEQUENCE_FILE, --in SEQUENCE_FILE — your input sequence file, in FASTA format. can be an assembled genome or transcriptome (DNA), or protein sequences from an annotated gene set. you can ALSO hand her a path to a directory holding multiple input files. multitasking queen 👑
• -o OUTPUT, --out OUTPUT — give your analysis run a recognisable short name. output folders and files get labelled with this name. > ⚠️ WARNING: do not provide a path. just the name. that's it. no paths. i'm serious bestie 😭
• -m MODE, --mode MODE — 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. pick your girl 💜
• --augustus — use the 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. one pair. one. 🙈
• --augustus_species AUGUSTUS_SPECIES — specify a species for Augustus training.
• --auto-lineage — run auto-lineage to find the optimum lineage path. she'll figure it out herself, independent queen ✨
• --auto-lineage-euk — run auto-placement just on the eukaryote tree to find the optimum lineage path.
• --auto-lineage-prok — run auto-lineage just on non-eukaryote trees to find the optimum lineage path.
• -c N, --cpu N — specify the number (N = integer) of threads/cores to use. give her cores, she gives you speed 🏃♀️
• --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 you use this together with other command line arguments, make sure to place this last. last means last, bestie.
• --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. no -f, no overwrite, she said what she said 💀
• -h, --help — show this help message and exit. the classic.
• --limit N — how many candidate regions (contig or transcript) to consider per BUSCO. (default: 3)
• --list-datasets — print the list of available BUSCO datasets. window shopping 🛍️
• --long — Optimization Augustus self-training mode. (Default: Off) adds considerably to the run time, but can improve results for some non-model organisms. the glow-up takes time, okay 😌
• --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. airplane mode but for datasets ✈️
• --out_path OUTPUT_PATH — optional location for the results folder, excluding the results folder name. Default is the current working directory.
• -q, --quiet — disable the info logs, displays only errors. minimalism era 🧘♀️
• -r, --restart — continue a run that had already partially completed. we don't start over in this house, we resume 💅
• --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. king behaviour, we love a contributor 🫶

and that's the whole page, bestie — busco 5.2.2, dated July 2021, served fresh from the BUSCO(1) manual. go benchmark something iconic. no cap, you got this 💖✨🎀🦋🌸💅