robsyme/busco repository overview

⁠BUSCO in docker

This is a repository that contains the BUSCO⁠ software for 'assessing genome assembly and annotation completeness with single-copy orthologs'. It contains preconfigured installations of the BUSCO prerequisites, including Augustus 3.0, hmmer, ncbi-blast+, and emboss.

⁠Using the container

Let's say I have my fungal genome scaffolds.fasta in the current directory, I can run busco by first downloading the profiles (in my case fungi):

wget http://busco.ezlab.org/files/fungi_buscos.tar.gz
tar -xzvf fungi_buscos.tar.gz && rm fungi_buscos.tar.gz

I can then run the busco docker container

docker run --rm -v $PWD:/in -w /in robsyme/busco \
    busco -in scaffolds.fasta -o my_run --lineage fungi

I might consider bundling in the profiles into lineage-specific docker images, but busco unhelpfully prepends a '.' to the lineage path, so I'd have to create a runner script that links in the profile folder into the current working directory, which is a bit messy. For the moment, I'm leaving the profiles to the user.