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

Homepage:

https://github.com/ComparativeGenomicsToolkit/Comparative-Annotation-Toolkit

License:

APACHE / Apache 2.0

Recipe:

/comparative-annotation-toolkit/meta.yaml

Links:

doi: 10.1101/231118

package comparative-annotation-toolkit

Versions:

0.1-2,  0.1-1,  0.1-0

Depends:

• augustus >=3.3

• bamtools

• bx-python >=0.7.1

• configobj >=5.0

• ete3

• frozendict

• luigi >=2.5

• numpy >=1.10

• pandas >=0.18

• pyfasta >=0.5.2

• pysam >=0.10

• python 2.7.*

• samtools >=1.3

• scipy >=0.18.1

• seaborn >=0.7

• sqlalchemy >=1.0

• toil >=3.5

• ucsc-axtchain

• ucsc-bamtopsl

• ucsc-bedsort

• ucsc-bedtobigbed

• ucsc-blat

• ucsc-chainmergesort

• ucsc-clustergenes

• ucsc-fatotwobit

• ucsc-genepredtobed

• ucsc-genepredtofakepsl

• ucsc-genepredtogtf

• ucsc-gff3togenepred

• ucsc-gtftogenepred

• ucsc-pslcdnafilter

• ucsc-pslcheck

• ucsc-pslmap

• ucsc-pslmappostchain

• ucsc-pslpostarget

• ucsc-pslrecalcmatch

• ucsc-psltobigpsl

• ucsc-transmappsltogenepred

Required By:

Installation

With an activated Bioconda channel (see 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 quay.io/biocontainers/comparative-annotation-toolkit:<tag>

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

Download stats

Link to this page

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