Docker container run environment for BUSCO (Benchmarking Universal Single-Copy Orthologs)

About BUSCO BUSCO v3 provides quantitative measures for the assessment of genome assembly, gene set, and transcriptome completeness, based on evolutionarily-informed expectations of gene content from near-universal single-copy orthologs selected from OrthoDB v9.

BUSCO assessments are implemented in open-source software, with a large selection of lineage-specific sets of Benchmarking Universal Single-Copy Orthologs. These conserved orthologs are ideal candidates for large-scale phylogenomics studies, and the annotated BUSCO gene models built during genome assessments provide a comprehensive gene predictor training set for use as part of genome annotation pipelines.

• http://busco.ezlab.org/

Usage

To run, mount your input directory with -v, and then use standard run_BUSCO.py commands. For example, to run the proteins annotation check (with -m proteins) on a fasta called seq.faa in the current directory, use the following:

docker run \
  -v "$PWD":/input \
  kastman/busco:3.0.0 \
  --in /input/seq.faa \
  -m proteins -o out_label -m proteins

You will probably want to grab the correct lineage profile from the Busco site. For example, to run with the high-level fungi dataset, first download the profile and then pass it as an argument when running.

lineage=fungi_odb9
wget http://busco.ezlab.org/datasets/$lineage.tar.gz
tar -xzvf $lineage.tar.gz && rm $lineage.tar.gz

docker run \
  -v "$PWD":/input \
  kastman/busco-docker:3.0.0 \
  --in /input/seq.faa \
  --lineage_path /input/$lineage
  -m proteins -o out_label -m proteins

For a complete list of available lineage profiles, see the full list on the BUSCO site or read the User Guide.

Note

Currently this docker repo contains only the 3.0.0 version, with and without R and ggplot2 for plotting (R adds about 400MB to the docker download so it is not included by default.)

To use the R container, specify it with the with_r suffix on the tag: kastman/busco-docker:3.0.0.with_r.

Reference

For more information, see:

BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs. Felipe A. Simão, Robert M. Waterhouse, Panagiotis Ioannidis, Evgenia V. Kriventseva, and Evgeny M. Zdobnov Bioinformatics, published online June 9, 2015 doi:10.1093/bioinformatics/btv351.