recipe comparative-annotation-toolkit

A straightforward end-to-end pipeline that takes as input a HAL-format multiple whole genome alignment as well as a GFF3 file representing annotations on one high quality assembly in the HAL alignment, and produces a output GFF3 annotation on all target genomes chosen



APACHE / Apache 2.0




doi: 10.1101/231118

package comparative-annotation-toolkit

(downloads) docker_comparative-annotation-toolkit



depends augustus:


depends bamtools:

depends bx-python:


depends configobj:


depends ete3:

depends frozendict:

depends luigi:


depends numpy:


depends pandas:


depends pyfasta:


depends pysam:


depends python:


depends samtools:


depends scipy:


depends seaborn:


depends sqlalchemy:


depends toil:


depends ucsc-axtchain:

depends ucsc-bamtopsl:

depends ucsc-bedsort:

depends ucsc-bedtobigbed:

depends ucsc-blat:

depends ucsc-chainmergesort:

depends ucsc-clustergenes:

depends ucsc-fatotwobit:

depends ucsc-genepredtobed:

depends ucsc-genepredtofakepsl:

depends ucsc-genepredtogtf:

depends ucsc-gff3togenepred:

depends ucsc-gtftogenepred:

depends ucsc-pslcdnafilter:

depends ucsc-pslcheck:

depends ucsc-pslmap:

depends ucsc-pslmappostchain:

depends ucsc-pslpostarget:

depends ucsc-pslrecalcmatch:

depends ucsc-psltobigpsl:

depends ucsc-transmappsltogenepred:



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 comparative-annotation-toolkit

and update with::

   mamba update comparative-annotation-toolkit

To create a new environment, run:

mamba create --name myenvname comparative-annotation-toolkit

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 `comparative-annotation-toolkit/tags`_ for valid values for ``<tag>``)

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