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BUSCO

Benchmarking Universal Single-Copy Orthologs (BUSCO) provides quantitative measures for the assessment of genome assembly, gene set, and transcriptomes.

BUSCO is available as a module on Apocrita.

Usage

To run the default installed version of BUSCO, simply load the busco module:

$ module load busco
$ BUSCO.py --help

usage: python BUSCO.py -i [SEQUENCE_FILE] -l [LINEAGE] \
                       -o [OUTPUT_NAME] -m [MODE] [OTHER OPTIONS]

For full usage documentation, run BUSCO.py --help.

Setting the Augustus configuration path

Please copy the Augustus configuration directory (/share/apps/centos7/augustus/<VERSION>/config) to an area you can write to and export AUGUSTUS_CONFIG_PATH variable before running BUSCO.

Example job

Serial job

Here is an example job running on 1 core and 1GB of memory executing the sample data provided in the sample_data sub-directory.

#!/bin/bash
#$ -cwd
#$ -j y
#$ -pe smp 1
#$ -l h_rt=1:0:0
#$ -l h_vmem=1G

module load busco

export AUGUSTUS_CONFIG_PATH=~/augustus_config
export BUSCO_SAMPLE_DATA=/share/apps/centos7/busco/<VERSION>/sample_data


BUSCO.py -i ${BUSCO_SAMPLE_DATA}/target.fa  \
         -o TEST \
         -l ${BUSCO_SAMPLE_DATA}/example/ \
         -m genome \
         -c ${NSLOTS}

Replace <VERSION> with the actual version of BUSCO you are running.

References