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LRScaf: improving draft genomes using long noisy reads.

ABSTRACT: BACKGROUND:The 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. RESULTS:We 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). CONCLUSIONS:The 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.

SUBMITTER: Qin M

PROVIDER: S-EPMC6902338 | biostudies-literature | 2019 Dec

REPOSITORIES: biostudies-literature

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LRScaf: improving draft genomes using long noisy reads.

Qin Mao M Wu Shigang S Li Alun A Zhao Fengli F Feng Hu H Ding Lulu L Ruan Jue J

BMC genomics 20191209 1

<h4>Background</h4>The 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, howeve ...[more]

PMID: 31818249

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Project description:BackgroundDe novo genome assembly using NGS data remains a computation-intensive task especially for large genomes. In practice, efficiency is often a primary concern and favors using a more efficient assembler like SOAPdenovo2. Yet SOAPdenovo2, based on de Bruijn graph, fails to take full advantage of longer NGS reads (say, 150 bp to 250 bp from Illumina HiSeq and MiSeq). Assemblers that are based on string graphs (e.g., SGA), though less popular and also very slow, are more favorable for longer reads.MethodsThis paper shows a new de novo assembler called BASE. It enhances the classic seed-extension approach by indexing the reads efficiently to generate adaptive seeds that have high probability to appear uniquely in the genome. Such seeds form the basis for BASE to build extension trees and then to use reverse validation to remove the branches based on read coverage and paired-end information, resulting in high-quality consensus sequences of reads sharing the seeds. Such consensus sequences are then extended to contigs.ResultsExperiments on two bacteria and four human datasets shows the advantage of BASE in both contig quality and speed in dealing with longer reads. In the experiment on bacteria, two datasets with read length of 100 bp and 250 bp were used.. Especially for the 250 bp dataset, BASE gives much better quality than SOAPdenovo2 and SGA and is simlilar to SPAdes. Regarding speed, BASE is consistently a few times faster than SPAdes and SGA, but still slower than SOAPdenovo2. BASE and Soapdenov2 are further compared using human datasets with read length 100 bp, 150 bp and 250 bp. BASE shows a higher N50 for all datasets, while the improvement becomes more significant when read length reaches 250 bp. Besides, BASE is more-meory efficent than SOAPdenovo2 when sequencing data with error rate.ConclusionsBASE is a practically efficient tool for constructing contig, with significant improvement in quality for long NGS reads. It is relatively easy to extend BASE to include scaffolding.

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LRScaf: improving draft genomes using long noisy reads.

Publications

LRScaf: improving draft genomes using long noisy reads.

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