SOAPdenovo-Trans: De novo transcriptome assembly with short RNA-Seq reads

TL;DR

SOAPdenovo-Trans is a novel de novo transcriptome assembler optimized for short RNA-Seq reads, demonstrating improved contiguity, reduced redundancy, and faster performance on datasets from rice and mouse.

Contribution

It introduces SOAPdenovo-Trans, a new algorithm specifically designed for RNA-Seq data, addressing challenges of short reads, alternative splicing, and variable expression levels.

Findings

Higher contiguity compared to existing methods

Lower redundancy in assembled transcripts

Faster execution time

Abstract

Motivation: Transcriptome sequencing has long been the favored method for quickly and inexpensively obtaining the sequences for a large number of genes from an organism with no reference genome. With the rapidly increasing throughputs and decreasing costs of next generation sequencing, RNA-Seq has gained in popularity; but given the typically short reads (e.g. 2 x 90 bp paired ends) of this technol- ogy, de novo assembly to recover complete or full-length transcript sequences remains an algorithmic challenge. Results: We present SOAPdenovo-Trans, a de novo transcriptome assembler designed specifically for RNA-Seq. Its performance was evaluated on transcriptome datasets from rice and mouse. Using the known transcripts from these well-annotated genomes (sequenced a decade ago) as our benchmark, we assessed how SOAPdenovo- Trans and two other popular software handle the practical issues of alternative splicing and variable expression levels. Our conclusion is that SOAPdenovo-Trans provides higher contiguity, lower redundancy, and faster execution. Availability and Implementation: Source code and user manual are at http://sourceforge.net/projects/soapdenovotrans/ Contact: xieyl@genomics.cn or bgi-soap@googlegroups.com