.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.15.
.TH BUSCO "1" "May 2020" "busco 4.0.6" "User Commands"
.SH NAME
busco \- benchmarking sets of universal single-copy orthologs
.SH SYNOPSIS
.B busco
\fB\-i\fR [SEQUENCE_FILE] \fB\-l\fR [LINEAGE] \fB\-o\fR [OUTPUT_NAME] \fB\-m\fR [MODE] [OTHER OPTIONS]
.SH DESCRIPTION
Assessing genome assembly and annotation completeness with Benchmarking
Universal Single-Copy Orthologs (BUSCO).
.SH OPTIONS
.TP
\fB\-i\fR FASTA FILE, \fB\-\-in\fR FASTA FILE
Input sequence file in FASTA format. Can be an assembled genome or transcriptome (DNA), or protein sequences from an annotated gene set.
.TP
\fB\-c\fR N, \fB\-\-cpu\fR N
Specify the number (N=integer) of threads/cores to use.
.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\-\-out_path\fR OUTPUT_PATH
Optional location for results folder, excluding results folder name. Default is current working directory.
.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\-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\-f\fR, \fB\-\-force\fR
Force rewriting of existing files. Must be used when output files with the provided name already exist.
.TP
\fB\-\-limit\fR REGION_LIMIT
How many candidate regions (contig or transcript) to consider per BUSCO (default: 3)
.TP
\fB\-\-long\fR
Optimization mode Augustus self\-training (Default: Off) adds considerably to the run time, but can improve results for some non\-model organisms
.TP
\fB\-q\fR, \fB\-\-quiet\fR
Disable the info logs, displays only errors
.TP
\fB\-\-augustus_parameters\fR AUGUSTUS_PARAMETERS
Pass additional arguments to Augustus. All arguments should be contained within a single pair of quotation marks, separated by commas. E.g. '\-\-param1=1,\-\-param2=2'
.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\-prok\fR
Run auto\-lineage just on non\-eukaryote trees 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\-\-update\-data\fR
Download and replace with last versions all lineages datasets and files necessary to their automated selection
.TP
\fB\-\-offline\fR
To indicate that BUSCO cannot attempt to download files
.TP
\fB\-\-config\fR CONFIG_FILE
Provide a config file
.TP
\fB\-v\fR, \fB\-\-version\fR
Show this version and exit
.TP
\fB\-h\fR, \fB\-\-help\fR
Show this help message and exit
.TP
\fB\-\-list\-datasets\fR
Print the list of available BUSCO datasets
.SH AUTHOR
 This manpage was written by Andreas Tille for the Debian distribution and
 can be used for any other usage of the program.