recipe braker3

BRAKER3 is the latest pipeline in the BRAKER suite



Other / Artistic License




doi: 10.1101/2023.01.13.524024

BRAKER3 enables the usage of RNA-seq and protein data in a fully automated pipeline to train and predict highly reliable genes with GeneMark-ETP and AUGUSTUS. The result of the pipeline is the combined gene set of both gene prediction tools, which only contains genes with very high support from extrinsic evidence.

package braker3

(downloads) docker_braker3



depends augustus:


depends bamtools:


depends biopython:

depends blast:


depends cdbtools:


depends compleasm:

depends diamond:


depends exonerate:


depends genomethreader:


depends makehub:

depends perl:

depends perl-app-cpanminus:

depends perl-class-data-inheritable:

depends perl-data-dumper:

depends perl-exception-class:

depends perl-file-homedir:

depends perl-file-spec:

depends perl-file-which:

depends perl-hash-merge:

depends perl-logger-simple:

depends perl-math-utils:

depends perl-mce:

depends perl-module-load-conditional:

depends perl-parallel-forkmanager:

depends perl-posix:

depends perl-scalar-list-utils:

depends perl-scalar-util-numeric:

depends perl-test-pod:

depends perl-yaml:

depends perl-yaml-libyaml:

depends python:


depends samtools:


depends spaln:


depends tsebra:



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 braker3

and update with::

   mamba update braker3

To create a new environment, run:

mamba create --name myenvname braker3

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<tag>

(see `braker3/tags`_ for valid values for ``<tag>``)


  • GeneMark software can be used for free, but requires a license file and should be additionally installed on the machine where the BRAKER3 environment is.

  • ProtHint software can be used for free, but doesn't allow redistribution and should be additionally installed on the machine where the BRAKER3 environment is.

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