LRScaf: improving draft genomes using long noisy reads
LRScaf: improving draft genomes using long noisy reads
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DOI：
10.1186/s12864-019-6337-2
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发表时间：
2019-12-09
期刊：
影响因子：
4.4
通讯作者：
Ruan, Jue
中科院分区：
文献类型：
--
作者：
Qin, Mao;Wu, Shigang;Ruan, Jue
背景：第三代测序（TGS）技术的出现为改善基因组组装打开了大门。长读段有望提高由下一代测序（NGS）技术构建的碎片化draft assemblies的质量。迄今为止，已经发布了一些能够改进草稿集的算法。有sspace - lonread、OPERA-LG、SMIS、npScarf、DBG2OLC、Unicycler和LINKS。然而，在大型基因组上进行杂交组装仍然具有挑战性。结果：我们开发了一种可扩展且计算效率高的支架，Long Reads scaffolder (LRScaf, https://github.com/shingocat/lrscaf)，它能够使用长读取显着提高组装的连续性。在这项研究中，我们总结了最先进的支架和LRScaf在大肠杆菌、葡萄球菌、拟南芥、sativa、pennellii、Z. mays和智人等7种生物上的综合性能评估。LRScaf显著提高了草案组件的连续性，例如，使用20倍覆盖的PacBio数据集将CHM1的NGA50值从127.1 kbp提高到9.4 Mbp，使用35倍覆盖的Nanopore数据集将NA12878的NGA50值从115.3 kbp提高到12.9 Mbp。此外，LRScaf在拟南芥（A. thaliana）、pennellii、Z. mays和H. sapens上产生的连续NGA50最好。此外，与其他支架相比，LRScaf具有最短的运行时间，并且LRScaf的峰值RAM对于大基因组仍然适用（例如，CHM1和NA12878上分别为20.3和62.6 GB）。结论：与其他支架算法相比，新算法LRScaf在最短的运行时间内获得了最好的或至少中等的支架连续性和准确性。此外，LRScaf提供了一种经济有效的方法来提高大基因组上草图组装的连续性。
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.