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


0.1-2, 0.1-1, 0.1-0

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



With an activated Bioconda channel (see 2. Set up channels), install with:

conda install comparative-annotation-toolkit

and update with:

conda update comparative-annotation-toolkit

or use the docker container:

docker pull<tag>

(see comparative-annotation-toolkit/tags for valid values for <tag>)