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Last pushed: 2 years ago
Short Description
BUSCO provides measures for assessment of assembly, gene set, and transcriptome completeness.
Full Description

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

I have a 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 would 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 will leave profile managment to the user.

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Owner
robsyme
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