recipe transdecoder

TransDecoder identifies candidate coding regions within transcript sequences, such as those generated by de novo RNA-Seq transcript assembly using Trinity, or constructed based on RNA-Seq alignments to the genome using Tophat and Cufflinks.


Developer docs:


Broad Institute



package transdecoder

(downloads) docker_transdecoder



depends bioconductor-seqlogo:

depends perl:

>=5.32.1,<6.0a0 *_perl5

depends perl-db-file:

depends perl-uri:

depends r-ggplot2:



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 transdecoder

and update with::

   mamba update transdecoder

To create a new environment, run:

mamba create --name myenvname transdecoder

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 `transdecoder/tags`_ for valid values for ``<tag>``)

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