SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler

By Ruibang Luo, Binghang Liu, Yinlong Xie, Zhenyu Li, Weihua Huang, Jianying Yuan, Guangzhu He, Yanxiang Chen, Qi Pan, Yunjie Liu and 20 more. GigaScience, 2012

4,725 citations recorded by the source corpus.

BackgroundThere is a rapidly increasing amount of de novo genome assembly using next-generation sequencing (NGS) short reads; however, several big challenges remain to be overcome in order for this to be efficient and accurate. SOAPdenovo has been successfully applied to assemble many published genomes, but it still needs improvement in continuity, accuracy and coverage, especially in repeat regions.FindingsTo overcome these challenges, we have developed its successor, SOAPdenovo2, which has the advantage of a new algorithm design that reduces memory consumption in graph construction, resolves more repeat regions in contig assembly, increases coverage and length in scaffold construction, improves gap closing, and optimizes for large genome.ConclusionsBenchmark using the Assemblathon1 and GAGE datasets showed that SOAPdenovo2 greatly surpasses its predecessor SOAPdenovo and is competitive to other assemblers on both assembly length and accuracy. We also provide an updated assembly version of the 2008 Asian (YH) genome using SOAPdenovo2. Here, the contig and scaffold N50 of the YH genome were ~20.9 kbp and ~22 Mbp, respectively, which is 3-fold and 50-fold longer than the first published version. The genome coverage increased from 81.16% to 93.91%, and memory consumption was ~2/3 lower during the point of largest memory consumption.

Subfields: Genetics, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/f8d1052e2c9d1cdd63093427ccc9169e848d777d

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Citations in the corpus

Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species (2013, methodology): “The de Bruijn approach was also used by the SOAPdenovo assembler [9] in generating the first wholly de novo assembly of a large eukaryotic genome sequence (the giant panda, Ailuropoda melanoleuca [10]).”
Dynamics and Stabilization of the Human Gut Microbiome during the First Year of Life. (2015, methodology): “De novo assembly of contigs and genomes To determine the best index for assembling high-quality reads into contigs (Luo et al., 2012), we tested the k-mer length ranging from 31bp to 49 bp by 2 bp for each sample.”
GetOrganelle: a fast and versatile toolkit for accurate de novo assembly of organelle genomes (2018, methodology): “For example, SPAdes [15], SOAPdenovo2 [16], and CLC Genomics Workbench (https://www.qiagen-bioinformatics.com/) have been widely used to assemble the WGS data, after which the organelle genomic scaffolds/contigs were selected or filtered out using a reference genome for further concatenation [17]…”
De novo assembly of bacterial transcriptomes from RNA-seq data (2015, result): “In order to evaluate Rockhopper 2 ’ s performance, we compared it with two leading de novo transcriptome as-semblers: Trinity version trinityrnaseq_r20140413p1 [8,25] and SOAPdenovo2 version 2.04 [10,26].”