.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.16.
.TH BUSCO "1" "July 2021" "busco 5.2.2" "User Commands"
.SH NAME
busco \- benchmarking sets of universal single-copy orthologs
.SH DESCRIPTION
usage: busco \fB\-i\fR [SEQUENCE_FILE] \fB\-l\fR [LINEAGE] \fB\-o\fR [OUTPUT_NAME] \fB\-m\fR [MODE] [OTHER OPTIONS]
.PP
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
.SS "optional arguments:"
.TP
\fB\-i\fR SEQUENCE_FILE, \fB\-\-in\fR 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.
.TP
\fB\-o\fR OUTPUT, \fB\-\-out\fR 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
.TP
\fB\-m\fR MODE, \fB\-\-mode\fR 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)
.TP
\fB\-l\fR LINEAGE, \fB\-\-lineage_dataset\fR LINEAGE
Specify the name of the BUSCO lineage to be used.
.TP
\fB\-\-augustus\fR
Use augustus gene predictor for eukaryote runs
.TP
\fB\-\-augustus_parameters\fR "\-\-PARAM1=VALUE1,\-\-PARAM2=VALUE2"
Pass additional arguments to Augustus. All arguments should be contained within a single pair of quotation marks, separated by commas.
.TP
\fB\-\-augustus_species\fR AUGUSTUS_SPECIES
Specify a species for Augustus training.
.TP
\fB\-\-auto\-lineage\fR
Run auto\-lineage to find optimum lineage path
.TP
\fB\-\-auto\-lineage\-euk\fR
Run auto\-placement just on eukaryote tree to find optimum lineage path
.TP
\fB\-\-auto\-lineage\-prok\fR
Run auto\-lineage just on non\-eukaryote trees to find optimum lineage path
.TP
\fB\-c\fR N, \fB\-\-cpu\fR N
Specify the number (N=integer) of threads/cores to use.
.TP
\fB\-\-config\fR CONFIG_FILE
Provide a config file
.TP
\fB\-\-datasets_version\fR DATASETS_VERSION
Specify the version of BUSCO datasets, e.g. odb10
.TP
\fB\-\-download\fR [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.
.TP
\fB\-\-download_base_url\fR DOWNLOAD_BASE_URL
Set the url to the remote BUSCO dataset location
.TP
\fB\-\-download_path\fR DOWNLOAD_PATH
Specify local filepath for storing BUSCO dataset downloads
.TP
\fB\-e\fR N, \fB\-\-evalue\fR N
E\-value cutoff for BLAST searches. Allowed formats, 0.001 or 1e\-03 (Default: 1e\-03)
.TP
\fB\-f\fR, \fB\-\-force\fR
Force rewriting of existing files. Must be used when output files with the provided name already exist.
.TP
\fB\-h\fR, \fB\-\-help\fR
Show this help message and exit
.TP
\fB\-\-limit\fR N
How many candidate regions (contig or transcript) to consider per BUSCO (default: 3)
.TP
\fB\-\-list\-datasets\fR
Print the list of available BUSCO datasets
.TP
\fB\-\-long\fR
Optimization Augustus self\-training mode (Default: Off); adds considerably to the run time, but can improve results for some non\-model organisms
.TP
\fB\-\-metaeuk_parameters\fR "\-\-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.
.TP
\fB\-\-metaeuk_rerun_parameters\fR "\-\-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.
.TP
\fB\-\-offline\fR
To indicate that BUSCO cannot attempt to download files
.TP
\fB\-\-out_path\fR OUTPUT_PATH
Optional location for results folder, excluding results folder name. Default is current working directory.
.TP
\fB\-q\fR, \fB\-\-quiet\fR
Disable the info logs, displays only errors
.TP
\fB\-r\fR, \fB\-\-restart\fR
Continue a run that had already partially completed.
.TP
\fB\-\-tar\fR
Compress some subdirectories with many files to save space
.TP
\fB\-\-update\-data\fR
Download and replace with last versions all lineages datasets and files necessary to their automated selection
.TP
\fB\-v\fR, \fB\-\-version\fR
Show this version and exit
.SH AUTHOR
 This manpage was written by Nilesh Patra for the Debian distribution and
 can be used for any other usage of the program.