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Overview
Busco assesses genome assembly and annotation completeness with Benchmarking Universal Single-Copy Orthologs.
Using
Use the module name busco to discover versions available and to load the application.
Example
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[]$ busco --help
usage: busco -i [SEQUENCE_FILE] -l [LINEAGE] -o [OUTPUT_NAME] -m [MODE] [OTHER OPTIONS]
Welcome to BUSCO 5.3.2: 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
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. The path to the output folder is set with --out_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 string with no white space, with each argument separated by a comma.
--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 string with no white space, with each argument separated by a comma.
--metaeuk_rerun_parameters "--PARAM1=VALUE1,--PARAM2=VALUE2"
Pass additional arguments to Metaeuk for the second run. All arguments should be contained within a single string with no white space, with each argument separated by a comma.
--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 |
Using Multiple Cores/Threads
The busco application allows you define multiple cores/threads within calls using the '-c or --cpu for number of threads allocated to the program' options.
After downloading the example files, a batch script would take the following form where we are defining and using 8 cores (on a single node).
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...
#SBATCH --cpus-per-task=8
...
busco -i ./test_data/bacteria/genome.fna -c 8 -m geno -f --out ./test_data/bacteria/test_eukaryota -l eukaryota_odb10 |
The best number of cores/threads and memory to use for a particular job will depend on the data and is up to the researcher to explore.
...
Multicore
The busco application allows you to define multiple cores/threads. For more details look at the busco --help and read the -c/--cpu options.