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BUSCO

Description

busco website

Assessing genome assembly and annotation completeness with Benchmarking Universal Single-Copy Orthologs

Environment Modules

Run module spider busco to find out what environment modules are available for this application.

Environment Variables

  • HPC_BUSCO_DIR - installation directory
  • HPC_BUSCO_BIN - executable directory
  • HPC_BUSCO_DAT - precomputed lineage data directory
  • HPC_BUSCO_CONF - sample config file

Additional Usage Information

Busco uses a config file which needs to be copied and modified to your needs.

$ cp $HPC_BUSCO_CONF/config.ini .
$ export BUSCO_CONFIG_FILE=$(pwd)/config.ini
$ busco -f -i ... <other arguments>

If you don't need to modify the config file you can use the installed copy:

$ busco -f --config ${HPC_BUSCO_CONF}/config.ini -i ... <other arguments>

Mandatory arguments.

-i or --in defines the input file to analyse which is either a nucleotide fasta file or a protein fasta file, depending on the BUSCO mode. As of v5.1.0 the input argument can now also be a directory containing fasta files to run in batch mode.
-o or --out defines the folder that will contain all results, logs, and intermediate data
-m or --mode sets the assessment MODE: genome, proteins, transcriptome
-l or --lineage_dataset

Datasets are located in /data/reference/busco/VERSION. The config.ini file is already configured to use the correct path.

Available datasets:

arthropoda
bacteria
eukaryota
fungi
metazoa
vertebrata

and many more. Run the following command to see all available species:

$ ls /data/reference/busco/VERSION
#for example: $ ls /data/reference/busco/v5

Example of busco run with metazoa dataset:

$ busco -f -in target.fa -o SAMPLE -l ${HPC_BUSCO_DAT}/metazoa -m genome

To allow busco to retrain an existing Augustus dataset, create a local copy of the data and set $AUGUSTUS_CONFIG_PATH variable to that path as explained on the Augustus page.

As an example, let's copy aspergillus_nidulans:

1. Load the busco module and copy augustus data

    $ mkdir -p augustus/species
    $ cp $AUGUSTUS_CONFIG_PATH/species/aspergillus_nidulans/ augustus/species/

2. Copy the models

    $ cp $AUGUSTUS_CONFIG_PATH/model augustus/

3. Add the export command to the busco job script and submit it.

    export AUGUSTUS_CONFIG_PATH=$(pwd)/augustus

Categories

biology, genomics