小柯机器人

美国约翰霍普金斯大学Sam Kovaka研究组取得最新进展。他通过使用UNCALLED（https://github.com/skovaka/UNCALLED）实时映射原始电信号进行靶向纳米孔测序。这一研究成果于2020年11月30日发表在《自然-生物技术》杂志上。

他们介绍了UNCALLED，这是一种开放源代码映射器，可将纳米孔电流信号流与相关序列快速匹配。UNCALLED随机地考虑了可以由信号表示的k-mers，然后根据Ferragina-Manzini索引中编码的相关候选物。他们使用UNCALLED消除了宏基因组学群体内已知细菌基因组的测序，使其余物种富集4.46倍。UNCALLED还使用一个MinION流动池将148个与遗传性癌症相关的人类基因富集至29.6x覆盖率，从而能够准确检测这些基因中的单核苷酸多态性、插入和缺失、结构变异和甲基化。

据介绍，传统的靶向测序方法消除了纳米孔测序的许多优势，例如能够准确检测结构变体或表观遗传修饰。ReadUntil方法允许纳米孔设备实时选择性地从孔中弹出读数，这可以实现纯粹的计算靶向测序。但是，这需要快速识别目标读取，而大多数映射方法都需要计算大量的碱基检出。

附：英文原文

Title: Targeted nanopore sequencing by real-time mapping of raw electrical signal with UNCALLED

Author: Sam Kovaka, Yunfan Fan, Bohan Ni, Winston Timp, Michael C. Schatz

Issue&Volume: 2020-11-30

Abstract: Conventional targeted sequencing methods eliminate many of the benefits of nanopore sequencing, such as the ability to accurately detect structural variants or epigenetic modifications. The ReadUntil method allows nanopore devices to selectively eject reads from pores in real time, which could enable purely computational targeted sequencing. However, this requires rapid identification of on-target reads while most mapping methods require computationally intensive basecalling. We present UNCALLED (https://github.com/skovaka/UNCALLED), an open source mapper that rapidly matches streaming of nanopore current signals to a reference sequence. UNCALLED probabilistically considers k-mers that could be represented by the signal and then prunes the candidates based on the reference encoded within a Ferragina–Manzini index. We used UNCALLED to deplete sequencing of known bacterial genomes within a metagenomics community, enriching the remaining species 4.46-fold. UNCALLED also enriched 148human genes associated with hereditary cancers to 29.6×coverage using one MinION flowcell, enabling accurate detection of single-nucleotide polymorphisms, insertions and deletions, structural variants and methylation in these genes.

DOI: 10.1038/s41587-020-0731-9

Source: https://www.nature.com/articles/s41587-020-0731-9

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