LRScaf: improving draft genomes using long noisy reads

Abstract

BackgroundThe advent of third-generation sequencing (TGS) technologies opens the door to improve genome assembly. Long reads are promising for enhancing the quality of fragmented draft assemblies constructed from next-generation sequencing (NGS) technologies. To date, a few algorithms that are capable of improving draft assemblies have released. There are SSPACE-LongRead, OPERA-LG, SMIS, npScarf, DBG2OLC, Unicycler, and LINKS. Hybrid assembly on large genomes remains challenging, however.ResultsWe develop a scalable and computationally efficient scaffolder, Long Reads Scaffolder (LRScaf, https://github.com/shingocat/lrscaf), that is capable of significantly boosting assembly contiguity using long reads. In this study, we summarise a comprehensive performance assessment for state-of-the-art scaffolders and LRScaf on seven organisms, i.e., E. coli, S. cerevisiae, A. thaliana, O. sativa, S. pennellii, Z. mays, and H. sapiens. LRScaf significantly improves the contiguity of draft assemblies, e.g., increasing the NGA50 value of CHM1 from 127.1 kbp to 9.4 Mbp using 20-fold coverage PacBio dataset and the NGA50 value of NA12878 from 115.3 kbp to 12.9 Mbp using 35-fold coverage Nanopore dataset. Besides, LRScaf generates the best contiguous NGA50 on A. thaliana, S. pennellii, Z. mays, and H. sapiens. Moreover, LRScaf has the shortest run time compared with other scaffolders, and the peak RAM of LRScaf remains practical for large genomes (e.g., 20.3 and 62.6 GB on CHM1 and NA12878, respectively).ConclusionsThe new algorithm, LRScaf, yields the best or, at least, moderate scaffold contiguity and accuracy in the shortest run time compared with other scaffolding algorithms. Furthermore, LRScaf provides a cost-effective way to improve contiguity of draft assemblies on large genomes.

Genome and transcriptome assemblies of the kuruma shrimp,Marsupenaeus japonicus

“…The polished assembly was broken into contigs using split.scaffolds.to.contigs.pl ( https://github.com/MadsAlbertsen/miscperlscripts/blob/master/split.scaffolds.to.contigs.pl ). The broken contigs were subjected to the first round of iterative scaffolding by the following programs: LRScaf v1.1.11 ( Qin et al 2019 ), using ONT long reads; BESST v2.2.8 ( Sahlin et al 2014 ), using Illumina mate-pair reads from all libraries; L_RNA_Scaffolder, using the transcriptome shotgun assembly and Iso-Seq cDNA sequences (aligned by BLAT v36). Each scaffolding was followed by gap-filling by TGS-GapCloser v1.1.1 and polishing by NtEdit v1.3.2.…”

A high-quality genome assembly and annotation of the European earwig Forficula auricularia

“…The purged genome underwent further scaffolding and gap-closing steps using Rails (v.1.5.1) and Cobbler (v.0.6.1) (Warren 2016), Lrscaf (v.1.1.11) (Qin et al . 2019) and Lrgapcloser (Xu et al .…”

A Deep Dive into Genome Assemblies of Non-vertebrate Animals

“…LoRMA [150], NaS [151], proovread [152] Long reads Canu [114], CONSENT [153], Daccord [154], FLAS [155], HALC [156], NextDenovo [121], MECAT [118], MECAT2 [118], NECAT [120] Polishing Short reads ntEdit [157], Pilon [158], POLCA [159] Short & long reads Apollo [160], Hapo-G [161], HyPo [162], Racon [163] Nanopolish [164], Quiver [165] Haplotig purging Long reads HaploMerger2 [166], purge dups [167], Purge Haplotigs [168] Scaffolding Short reads Bambus [169], BATISCAF [170], BESST [171], BOSS [172], Mate pairs GRASS [173], MIP [174], Opera [175], ScaffMatch [176], ScaffoldScaffolder [177], SCARPA [178], SCOP [179], SLIQ [180], SOPRA [181], SSPACE [182], WiseScaffolder [183] Long reads DENTIST [184], LINKS [185], LRScaf [186], npScarf [187], PBJelly [188], RAILS [189], SLR [190],...…”