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

By Yinlong Xie, Gengxiong Wu, Jingbo Tang, Ruibang Luo, Jordan Patterson, Shanlin Liu, Weihua Huang, Guangzhu He, Shengchang Gu, Sheng-qiang Li and 6 more. Bioinform., 2013

863 citations recorded by the source corpus.

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/.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/d67a93295497578e114125a2e5e1041a1ec91fb4

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Citations in the corpus

Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie, and Ballgown (2016, methodology): “Several methods can reconstruct transcripts de novo , without the use of a reference genome 14–16 , a different problem from the one considered in this protocol.”
A survey of best practices for RNA-seq data analysis (2016, methodology): “We refer the reader to [30] for a comprehensive comparison of RNA-seq mappers.”
Data access for the 1,000 Plants (1KP) project (2014, methodology): “Our RNA extraction protocols [3] and our RNA-Seq transcriptome assembly algorithms [4] have already been published.”
rnaSPAdes: a de novo transcriptome assembler and its application to RNA-Seq data (2018, neutral): “To address these constraints, de novo transcriptome assemblers [7–11] have emerged as a viable complement to the reference-based tools.”
Gaining comprehensive biological insight into the transcriptome by performing a broad-spectrum RNA-seq analysis (2017, methodology): “Due to better memory usage, we analysed SOAPdenovo-Trans on the whole MCF7-300 and NA12878 samples as well (SOAPdenovo-Trans-ALL).”
Evolutionary History of the Hymenoptera. (2017, methodology): “01) [29], the assembled transcripts were filtered for possible contaminants, and the raw reads and filtered assemblies were submitted to the NCBI SRA and TSA archives.”