recipe pasa

PASA, acronym for Program to Assemble Spliced Alignments (and pronounced 'pass-uh'), is a eukaryotic genome annotation tool that exploits spliced alignments of expressed transcript sequences to automatically model gene structures, and to maintain gene structure annotation consistent with the most recently available experimental sequence data. PASA also identifies and classifies all splicing variations supported by the transcript alignments.

Homepage

https://pasapipeline.github.io/

License

Broad Institute

Recipe

/pasa/meta.yaml

Links

doi: 10.1186/gb-2008-9-1-r7

package pasa

Versions

2.4.1-1,  2.4.1-0,  2.3.3-2,  2.3.3-1,  2.3.3-0

Depends

• blat

• cdbtools

• fasta3

• gmap 2017.11.15

• libgcc-ng >=9.3.0

• libstdcxx-ng >=9.3.0

• lighttpd

• perl

• perl-cgi

• perl-db-file

• perl-dbd-sqlite

• perl-uri

• r-base

• samtools

• slclust

• transdecoder >=5.5.0

Required By

• funannotate

Installation

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

conda install pasa

and update with:

conda update pasa

or use the docker container:

docker pull quay.io/biocontainers/pasa:<tag>

(see pasa/tags for valid values for <tag>)

Link to this page

Render an badge with the following MarkDown:

[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/pasa/README.html)