NAME¶

busco - benchmarking sets of universal single-copy orthologs

SYNOPSIS¶

busco -i [SEQUENCE_FILE] -l [LINEAGE] -o [OUTPUT_NAME] -m [MODE] [OTHER OPTIONS]

DESCRIPTION¶

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

OPTIONS¶

-i FASTA FILE, --in FASTA FILE

Input sequence file in FASTA format. Can be an assembled genome or transcriptome (DNA), or protein sequences from an annotated gene set.

-c N, --cpu N

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

-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

--out_path OUTPUT_PATH

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

-e N, --evalue N

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

-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.

-f, --force

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

--limit REGION_LIMIT

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

--long

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

-q, --quiet

Disable the info logs, displays only errors

--augustus_parameters 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'

--augustus_species AUGUSTUS_SPECIES

Specify a species for Augustus training.

--auto-lineage

Run auto-lineage to find optimum lineage path

--auto-lineage-prok

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

--auto-lineage-euk

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

--update-data

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

--offline

To indicate that BUSCO cannot attempt to download files

--config CONFIG_FILE

Provide a config file

-v, --version

Show this version and exit

-h, --help

Show this help message and exit

--list-datasets

Print the list of available BUSCO datasets

AUTHOR¶

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