ClusTrast: a short read de novo transcript isoform assembler guided by clustered contigs.

ABSTRACT:

Background

Transcriptome assembly from RNA-sequencing data in species without a reliable reference genome has to be performed de novo, but studies have shown that de novo methods often have inadequate ability to reconstruct transcript isoforms. We address this issue by constructing an assembly pipeline whose main purpose is to produce a comprehensive set of transcript isoforms.

Results

We present the de novo transcript isoform assembler ClusTrast, which takes short read RNA-seq data as input, assembles a primary assembly, clusters a set of guiding contigs, aligns the short reads to the guiding contigs, assembles each clustered set of short reads individually, and merges the primary and clusterwise assemblies into the final assembly. We tested ClusTrast on real datasets from

SUBMITTER: Westrin KJ 

PROVIDER: S-EPMC10836024 | biostudies-literature | 2024 Feb

REPOSITORIES: biostudies-literature