Roast: a tool for reference-free optimization of supertranscriptome assemblies.

ABSTRACT:

Background

Transcriptomic studies involving organisms for which reference genomes are not available typically start by generating de novo transcriptome or supertranscriptome assembly from the raw RNA-seq reads. Assembling a supertranscriptome is, however, a challenging task due to significantly varying abundance of mRNA transcripts, alternative splicing, and sequencing errors. As a result, popular de novo supertranscriptome assembly tools generate assemblies containing contigs that are partially-assembled, fragmented, false chimeras or have local mis-assemblies leading to decreased assembly accuracy. Commonly available tools for assembly improvement rely primarily on running BLAST using closely related species making their accuracy and reliability conditioned on the availability of

SUBMITTER: Shabbir M 

PROVIDER: S-EPMC10763045 | biostudies-literature | 2024 Jan

REPOSITORIES: biostudies-literature