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BUSCO(1) User Commands BUSCO(1)


busco - benchmarking sets of universal single-copy orthologs




Assessing genome assembly and annotation completeness with Benchmarking Universal Single-Copy Orthologs (BUSCO).


Input sequence file in FASTA format. Can be an assembled genome or transcriptome (DNA), or protein sequences from an annotated gene set.
Specify the number (N=integer) of threads/cores to use.
Give your analysis run a recognisable short name. Output folders and files will be labelled with this name. WARNING: do not provide a path
Optional location for results folder, excluding results folder name. Default is current working directory.
E-value cutoff for BLAST searches. Allowed formats, 0.001 or 1e-03 (Default: 1e-03)
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)
Specify the name of the BUSCO lineage to be used.
Force rewriting of existing files. Must be used when output files with the provided name already exist.
How many candidate regions (contig or transcript) to consider per BUSCO (default: 3)
Optimization mode Augustus self-training (Default: Off) adds considerably to the run time, but can improve results for some non-model organisms
Disable the info logs, displays only errors
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'
Specify a species for Augustus training.
Run auto-lineage to find optimum lineage path
Run auto-lineage just on non-eukaryote trees to find optimum lineage path
Run auto-placement just on eukaryote tree to find optimum lineage path
Download and replace with last versions all lineages datasets and files necessary to their automated selection
To indicate that BUSCO cannot attempt to download files
Provide a config file
Show this version and exit
Show this help message and exit
Print the list of available BUSCO datasets


This manpage was written by Andreas Tille for the Debian distribution and
can be used for any other usage of the program.

May 2020 busco 4.0.6