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

Abstract

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.

The genome of the recently domesticated crop plant sugar beet (Beta vulgaris)

“…Gap closing was performed using 670 million Illumina paired-end reads generated from two PCR-amplified libraries with insert sizes 600 nt and 250 nt, and from five PCR-free libraries with insert sizes 200-700 nt as input for GapCloser 20 (v1.12-r6, default parameters and -p set to 31). Fig.…”

A reference genome of the Chinese hamster based on a hybrid assembly strategy

“…The RefSeq reference genome of the Chinese hamster is based on the SOAPdenovo2 [Luo et al, 2012] assembly [Lewis et al, 2013]. The different paired-end and mate-pair Illumina libraries were assembled using SOAPdenovo2 [Luo et al, 2012].…”

Genome comparisons indicate recent transfer ofwRi‐likeWolbachiabetween sister speciesDrosophila suzukiiandD. subpulchrella

“…To assemble w Spc, we initially cleaned, trimmed, and assembled reads for the Wolbachia ‐infected D. subpulchrella using Sickle (https://github.com/najoshi/sickle) and SOAPdenovo v. 2.04 (Luo et al., 2012). For the assembly, K values of 31, 41, …, 101 were tried, and the best assembly (fewest contigs and largest N50) was kept.…”

“…The D. suzukii and D. subpulchrella reads were aligned to the w Spc assembly with bwa 0.7.12 (Li & Durbin, 2009). For both contigs that contain part of the WRi_006720 gene, reads mapping to the ISWpi7 transposable element plus the neighboring 500 bp were extracted and assembled with SOAPdenovo v. 2.04 (Luo et al., 2012), using a K value of 55. Both the D. suzukii and D. subpulchrella reads assembled into a single contig containing the two pieces of WRi_006720 interrupted by a single copy of ISWpi7.…”