CAARS: comparative assembly and annotation of RNA-Seq data.

ABSTRACT:

Motivation

RNA sequencing (RNA-Seq) is a widely used approach to obtain transcript sequences in non-model organisms, notably for performing comparative analyses. However, current bioinformatic pipelines do not take full advantage of pre-existing reference data in related species for improving RNA-Seq assembly, annotation and gene family reconstruction.

Results

We built an automated pipeline named CAARS to combine novel data from RNA-Seq experiments with existing multi-species gene family alignments. RNA-Seq reads are assembled into transcripts by both de novo and assisted assemblies. 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

SUBMITTER: Rey C 

PROVIDER: S-EPMC6596894 | biostudies-literature | 2019 Jul

REPOSITORIES: biostudies-literature