Assembling large genomes with single-molecule sequencing and locality-sensitive hashing
Assembling large genomes with single-molecule sequencing and locality-sensitive hashing
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DOI：
10.1038/nbt.3238
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发表时间：
2015-06-01
影响因子：
46.9
通讯作者：
Phillippy, Adam M.
中科院分区：
文献类型：
--
作者：
Berlin, Konstantin;Koren, Sergey;Phillippy, Adam M.
长时间阅读，单分子实时(SMRT)测序通常用于完成微生物基因组，但现有的组装方法并没有很好地扩展到更大的基因组。我们引入了MinHash对齐过程(MHAP)，用于使用概率、位置敏感的散列来处理重叠的噪声较长的读取。将MHAP与Celera组装器整合后，能够从SMRT测序中获得酿酒酵母、拟南芥、黑腹果蝇和人葡萄胎细胞系(CHM1)的参考级从头组装。由此产生的组装是高度连续的，包括完全分解的染色体臂和关闭这些参考基因组中的持久间隙。我们的黑腹葡萄球菌的组装揭示了以前未知的异染色质和端粒转换序列，我们从CHM1组装了低复杂性的序列，填补了人类GRCh38参考文献中的空白。使用MHAP和Celera组装器，单分子测序可以产生从头开始的接近完整的真核组件，与现有的参考基因组相比，准确率为99.99%。
Long-read, single-molecule real-time (SMRT) sequencing is routinely used to finish microbial genomes, but available assembly methods have not scaled well to larger genomes. We introduce the MinHash Alignment Process (MHAP) for overlapping noisy, long reads using probabilistic, locality-sensitive hashing. Integrating MHAP with the Celera Assembler enabled reference-grade de novo assemblies of Saccharomyces cerevisiae, Arabidopsis thaliana, Drosophila melanogaster and a human hydatidiform mole cell line (CHM1) from SMRT sequencing. The resulting assemblies are highly continuous, include fully resolved chromosome arms and close persistent gaps in these reference genomes. Our assembly of D. melanogaster revealed previously unknown heterochromatic and telomeric transition sequences, and we assembled low-complexity sequences from CHM1 that fill gaps in the human GRCh38 reference. Using MHAP and the Celera Assembler, single-molecule sequencing can produce de novo near-complete eukaryotic assemblies that are 99.99% accurate when compared with available reference genomes.