Targeted nanopore sequencing by real-time mapping of raw electrical signal with UNCALLED.
Targeted nanopore sequencing by real-time mapping of raw electrical signal with UNCALLED.
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DOI：
10.1038/s41587-020-0731-9
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发表时间：
2021-04
影响因子：
46.9
通讯作者：
Schatz MC
中科院分区：
文献类型：
--
作者：
Kovaka S;Fan Y;Ni B;Timp W;Schatz MC
传统的靶向测序方法消除了纳米孔测序的许多好处，例如准确检测结构变异(SVS)或表观遗传修饰的能力。ReadUntil方法允许纳米孔设备实时选择性地从孔中排出读数，这可以实现纯粹的计算靶向测序。然而，这需要快速识别目标上的读取，并且大多数映射方法需要计算密集的基本计算。我们提供了一个开放源码的映射器，它可以将流动的纳米孔电流信号与参考序列进行快速匹配。未被叫概率地考虑信号可以表示的k-MERS，然后基于在FM索引中编码的参考来剪枝候选。我们使用unCall来耗尽一个元基因组社区内已知细菌基因组的测序，使剩余物种丰富了4.46倍。UNCALL还使用一个小流动细胞将148个与遗传性癌症相关的人类基因丰富到29.6倍，从而能够准确检测这些基因中的SNPs、INDELS、SVS和甲基化。
Conventional targeted sequencing methods eliminate many of the benefits of nanopore sequencing, such as the ability to accurately detect structural variants (SVs) 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, and most mapping methods require computationally intensive basecalling. We present UNCALLED (github.com/skovaka/UNCALLED), an open-source mapper that rapidly matches streaming nanopore current signals to a reference sequence. UNCALLED probabilistically considers k-mers that the signal could represent, and then prunes the candidates based on the reference encoded within an FM-index. We used UNCALLED to deplete sequencing of known bacterial genomes within a metagenomics community, enriching the remaining species by 4.46 fold. UNCALLED also enriched 148 human genes associated with hereditary cancers to 29.6x coverage using one MinION flowcell, enabling accurate detection of SNPs, indels, SVs, and methylation in these genes.
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影响因子：
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作者：
Gardner EJ;Lam VK;Harris DN;Chuang NT;Scott EC;Pittard WS;Mills RE;1000 Genomes Project Consortium;Devine SE
通讯作者：
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作者：
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