busco1

optional arguments:

-i SEQUENCE_FILE, --in 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.

-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

-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.

--augustus

Use 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.

--augustus_species AUGUSTUS_SPECIES

Specify a species for Augustus training.

--auto-lineage

Run auto-lineage to find optimum lineage path

--auto-lineage-euk

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

--auto-lineage-prok

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

-c N, --cpu N

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

--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 used together with other command line arguments, make sure to place this last.

--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.

-h, --help

Show this help message and exit

--limit N

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

--list-datasets

Print the list of available BUSCO datasets

--long

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

--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

--out_path OUTPUT_PATH

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

-q, --quiet

Disable the info logs, displays only errors

-r, --restart

Continue a run that had already partially completed.

--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