SOAPdenovo-Trans: <i>de novo</i> transcriptome assembly with short RNA-Seq reads

TLDR

Transcriptome sequencing, especially RNA‑Seq, is a rapid, cost‑effective way to obtain gene sequences from organisms lacking reference genomes, but the short read lengths of next‑generation sequencing pose significant challenges for de novo assembly of full‑length transcripts. The authors benchmarked SOAPdenovo‑Trans on rice and mouse transcriptomes, comparing it to two other popular assemblers using known reference transcripts to evaluate handling of alternative splicing and variable expression. SOAPdenovo‑Trans achieved higher contiguity, lower redundancy, and faster execution than the compared assemblers. Source code, user manual, and supplementary data are available at http://sourceforge.net/projects/soapdenovotrans/ (contact [e-mail] or [e-mail]).

Abstract

Abstract Motivation: Transcriptome sequencing has long been the favored method for quickly and inexpensively obtaining a large number of gene sequences from an organism with no reference genome. Owing to the rapid increase in throughputs and decrease in costs of next- generation sequencing, RNA-Seq in particular has become the method of choice. However, the very short reads (e.g. 2 × 90 bp paired ends) from next generation sequencing makes de novo assembly to recover complete or full-length transcript sequences an algorithmic challenge. Results: Here, we present SOAPdenovo-Trans, a de novo transcriptome assembler designed specifically for RNA-Seq. We evaluated its performance on transcriptome datasets from rice and mouse. Using as our benchmarks the known transcripts from these well-annotated genomes (sequenced a decade ago), we assessed how SOAPdenovo-Trans and two other popular transcriptome assemblers handled such practical issues as 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 available at http://sourceforge.net/projects/soapdenovotrans/. Contact: [e-mail] or [e-mail] Supplementary information: Supplementary data are available at Bioinformatics online.