recipe busco

Assessment of assembly completeness using Universal Single Copy Orthologs

Homepage:

https://busco.ezlab.org/

Developer docs:

https://gitlab.com/ezlab/busco

License:

MIT / MIT

Recipe:

/busco/meta.yaml

Links:

biotools: busco, doi: 10.1093/bioinformatics/btv351, usegalaxy-eu: busco

BUSCO provides measures for quantitative 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.

package busco

(downloads) docker_busco

versions:
5.6.1-05.6.0-05.5.0-05.4.7-05.4.6-05.4.5-05.4.4-05.4.3-05.4.2-0

5.6.1-05.6.0-05.5.0-05.4.7-05.4.6-05.4.5-05.4.4-05.4.3-05.4.2-05.4.1-05.4.0-25.4.0-15.4.0-05.3.2-05.3.1-05.3.0-05.2.2-05.2.1-05.2.0-05.1.3-05.1.2-05.1.1-15.1.1-05.1.0-15.1.0-05.0.0-15.0.0-04.1.4-24.1.4-14.1.4-04.1.3-04.1.2-34.1.2-24.1.2-14.1.2-04.1.1-04.0.6-04.0.5-04.0.4-14.0.4-04.0.2-04.0.1-04.0.0-04.0.beta1-03.0.2-133.0.2-123.0.2-113.0.2-103.0.2-93.0.2-83.0.2-73.0.2-63.0.2-53.0.2-43.0.1-02.0.1-02.0-01.2-11.2-0

depends augustus:

>=3.3

depends bbmap:

depends biopython:

depends blast:

>=2.10.1

depends dendropy:

<4.6.0

depends fonts-conda-ecosystem:

depends hmmer:

>=3.1b2

depends metaeuk:

>=6.a5d39d9

depends miniprot:

depends pandas:

depends prodigal:

depends python:

>=3.3

depends r-base:

depends r-ggplot2:

>=2.2.1

depends requests:

depends sepp:

>=4.3.10

depends wget:

requirements:

Installation

You need a conda-compatible package manager (currently either micromamba, mamba, or conda) and the Bioconda channel already activated (see set-up-channels).

While any of above package managers is fine, it is currently recommended to use either micromamba or mamba (see here for installation instructions). We will show all commands using mamba below, but the arguments are the same for the two others.

Given that you already have a conda environment in which you want to have this package, install with:

   mamba install busco

and update with::

   mamba update busco

To create a new environment, run:

mamba create --name myenvname busco

with myenvname being a reasonable name for the environment (see e.g. the mamba docs for details and further options).

Alternatively, use the docker container:

   docker pull quay.io/biocontainers/busco:<tag>

(see `busco/tags`_ for valid values for ``<tag>``)

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