CAARS: comparative assembly and annotation of RNA-Seq data.MOTIVATION
 We built an automated pipeline named CAARS to combine novel data from RNA-Seq experiments with existing multi-species gene family alignments.  Then, CAARS incorporates transcripts into gene families, builds gene alignments and trees and uses phylogenetic information to classify the genes as orthologs and paralogs of existing genes.  We used CAARS to assemble and annotate RNA-Seq data in rodents and fishes using distantly related genomes as reference, a difficult case for this kind of analysis.  We showed CAARS assemblies are more complete and accurate than those assembled by a standard pipeline consisting of de novo assembly coupled with annotation by sequence similarity on a guide species.  In addition to annotated transcripts, CAARS provides gene family alignments and trees, annotated with orthology relationships, directly usable for downstream comparative analyses.


 CAARS is implemented in Python and Ocaml and is freely available at https://github.com/carinerey/caars.



CAARS