Strawberry: Fast and accurate genome-guided transcript reconstruction and quantification from RNA-Seq.

ABSTRACT: We propose a novel method and software tool, Strawberry, for transcript reconstruction and quantification from RNA-Seq data under the guidance of genome alignment and independent of gene annotation. Strawberry consists of two modules: assembly and quantification. The novelty of Strawberry is that the two modules use different optimization frameworks but utilize the same data graph structure, which allows a highly efficient, expandable and accurate algorithm for dealing large data. The assembly module parses aligned reads into splicing graphs, and uses network flow algorithms to select the most likely transcripts. The quantification module uses a latent class model to assign read counts from the nodes of splicing graphs to transcripts. Strawberry simultaneously estimates the transcript abun

SUBMITTER: Liu R 

PROVIDER: S-EPMC5720828 | biostudies-literature | 2017 Nov

REPOSITORIES: biostudies-literature