Icarust, a real-time simulator for Oxford Nanopore adaptive sampling
Icarust, a real-time simulator for Oxford Nanopore adaptive sampling
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Icarust，牛津纳米孔自适应采样的实时模拟器
DOI：
10.1101/2023.05.16.540986
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发表时间：
2023
期刊：
影响因子：
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通讯作者：
Munro R
中科院分区：
文献类型：
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作者：
Munro R
动机Oxford Nanopore Technologies (ONT) 测序仪能够实时生成序列数据，从而允许在运行期间进行并发分析。自适应采样在极端情况下利用这种实时功能，根据从每次读取开始时对序列的评估来拒绝或接受测序读取。该功能由 ONT 的软件 MinKNOW（Oxford Nanopore Technologies）提供。设计和开发利用自适应采样的软件在测序耗材、使用珍贵样本和准备测序文库方面可能成本高昂。 MinKNOW 通过允许重放之前排序的运行进行测试来部分解决这个问题。然而，正如我们所展示的，排序输出仅响应自适应采样指令而发生部分变化。在这里，我们介绍了 Icarust，这是一种能够更准确地近似测序运行的工具。 Icarust 重新创建 MinKNOW 所需的所有端点来执行自适应采样，并写入与当前碱基调用者和分析管道兼容的输出。 Icarust 提供纳米孔信号，使用 R9 或 R10 孔模型从任何参考基因组模拟 MinION 或 PromethION 流动细胞实验。我们表明，使用 Icarust 模拟测序运行为利用纳米孔测序实时特性的软件提供了一个真实的测试和开发环境。可用性和实施所有代码都是开源的，可以在此处免费获取 - https://github.com/LooseLab/Icarust。 Icarust 是用 Rust 实现的，还提供了 docker 容器。本文所依据的数据将根据合理请求分享给通讯作者。
MotivationOxford Nanopore Technologies (ONT) sequencers enable real-time generation of sequence data, which allows for concurrent analysis during a run. Adaptive sampling leverages this real-time capabilityin extremis, rejecting or accepting reads for sequencing based on assessment of the sequence from the start of each read. This functionality is provided by ONT’s software, MinKNOW (Oxford Nanopore Technologies). Designing and developing software to take advantage of adaptive sampling can be costly in terms of sequencing consumables, using precious samples and preparing sequencing libraries. MinKNOW addresses this in part by allowing the replay of previously sequenced runs for testing. However, as we show, the sequencing output only partially changes in response to adaptive sampling instructions. Here we present Icarust, a tool enabling more accurate approximations of sequencing runs. Icarust recreates all the required endpoints of MinKNOW to perform adaptive sampling and writes output compatible with current base-callers and analysis pipelines. Icarust serves nanopore signal simulating a MinION or PromethION flow cell experiment from any reference genome using either R9 or R10 pore models. We show that simulating sequencing runs with Icarust provides a realistic testing and development environment for software exploiting the real-time nature of Nanopore sequencing.Availability and implementationAll code is open source and freely available here—https://github.com/LooseLab/Icarust. Icarust is implemented in Rust, with a docker container also available. The data underlying this article will be shared on reasonable request to the corresponding author.