美国加州大学圣克鲁斯分校Benedict Paten及其课题组，利用纳米孔测序和Shasta工具包完成了对11个人类基因组的高效从头组装。2020年5月4日的《自然-生物技术》在线发表了这项成果。
为了实现快速的人类基因组组装，研究人员开发了Shasta（一种从头开始的长读组装器）以及名为MarginPolish和HELEN的抛光算法。使用单个PromethION纳米孔测序仪和Shasta工具包，研究人员在9 d内从头组装了11个高度连续的人基因组。
研究人员在每个样品的三个流动池，获得了约63倍的覆盖范围、42 kb的N50读数值和6.5倍100 kb以上的读数覆盖率。在单个商业计算节点上，Shasta在6小时内完成了人完整的单倍体基因组组装。
MarginPolish和HELEN抛光的单倍体组件与单纳米孔读数的同一性超过99.9％（Phred质量得分QV = 30）。另外，通过邻近连接测序可以在近染色体水平对这11个基因组进行组装。研究人员将Shasta与现有二倍体、单倍体和三重结合人类样品的方法进行了比较，揭示了其更高的准确性和速度。
据悉，已经报道使用纳米孔长读长测序的方法从头组装人类基因组，但是它花费了超过150,000 CPU小时和数周的计算使用时间。
附：英文原文
Title: Nanopore sequencing and the Shasta toolkit enable efficient de novo assembly of eleven human genomes
Author: Kishwar Shafin, Trevor Pesout, Ryan Lorig-Roach, Marina Haukness, Hugh E. Olsen, Colleen Bosworth, Joel Armstrong, Kristof Tigyi, Nicholas Maurer, Sergey Koren, Fritz J. Sedlazeck, Tobias Marschall, Simon Mayes, Vania Costa, Justin M. Zook, Kelvin J. Liu, Duncan Kilburn, Melanie Sorensen, Katy M. Munson, Mitchell R. Vollger, Jean Monlong, Erik Garrison, Evan E. Eichler, Sofie Salama, David Haussler, Richard E. Green, Mark Akeson, Adam Phillippy, Karen H. Miga, Paolo Carnevali, Miten Jain, Benedict Paten
Issue&Volume: 2020-05-04
Abstract: De novo assembly of a human genome using nanopore long-read sequences has been reported, but it used more than 150,000CPU hours and weeks of wall-clock time. To enable rapid human genome assembly, we present Shasta, a de novo long-read assembler, and polishing algorithms named MarginPolish and HELEN. Using a single PromethION nanopore sequencer and our toolkit, we assembled 11 highly contiguous human genomes de novo in 9d. We achieved roughly 63× coverage, 42-kb read N50 values and 6.5× coverage in reads >100kb using three flow cells per sample. Shasta produced a complete haploid human genome assembly in under 6h on a single commercial compute node. MarginPolish and HELEN polished haploid assemblies to more than 99.9% identity (Phred quality score QV=30) with nanopore reads alone. Addition of proximity-ligation sequencing enabled near chromosome-level scaffolds for all 11 genomes. We compare our assembly performance to existing methods for diploid, haploid and trio-binned human samples and report superior accuracy and speed.
DOI: 10.1038/s41587-020-0503-6
Source: https://www.nature.com/articles/s41587-020-0503-6
Nature Biotechnology：《自然—生物技术》，创刊于1996年。隶属于施普林格·自然出版集团，最新IF：68.164
官方网址：https://www.nature.com/nbt/
投稿链接：https://mts-nbt.nature.com/cgi-bin/main.plex
本期文章：《自然—生物技术》：Online/在线发表
