Faculty of Mathematics, Physics and Informatics, Comenius University in Bratislava, Mlynská dolina, Bratislava, Slovakia.
Bioinformatics. 2020 Aug 15;36(14):4191-4192. doi: 10.1093/bioinformatics/btaa297.
Oxford Nanopore MinION is a portable DNA sequencer that is marketed as a device that can be deployed anywhere. Current base callers, however, require a powerful GPU to analyze data produced by MinION in real time, which hampers field applications.
We have developed a fast base caller DeepNano-blitz that can analyze stream from up to two MinION runs in real time using a common laptop CPU (i7-7700HQ), with no GPU requirements. The base caller settings allow trading accuracy for speed and the results can be used for real time run monitoring (i.e. sample composition, barcode balance, species identification, etc.) or prefiltering of results for more detailed analysis (i.e. filtering out human DNA from human-pathogen runs).
DeepNano-blitz has been developed and tested on Linux and Intel processors and is available under MIT license at https://github.com/fmfi-compbio/deepnano-blitz.
Supplementary data are available at Bioinformatics online.
牛津纳米孔 MinION 是一种便携式 DNA 测序仪，其市场定位是可在任何地方部署的设备。然而，目前的碱基调用器需要强大的 GPU 才能实时分析 MinION 产生的数据，这阻碍了现场应用。
我们开发了一种快速的碱基调用器 DeepNano-blitz，它可以使用普通笔记本电脑 CPU（i7-7700HQ）实时分析多达两个 MinION 运行的流，无需 GPU 要求。碱基调用器设置允许在准确性和速度之间进行权衡，结果可用于实时运行监控（即样本组成、条形码平衡、物种鉴定等）或对结果进行预过滤以进行更详细的分析（例如，从人病原体运行中过滤出人 DNA）。
DeepNano-blitz 已在 Linux 和 Intel 处理器上进行了开发和测试，并在 MIT 许可证下可在 https://github.com/fmfi-compbio/deepnano-blitz 获得。
补充数据可在“Bioinformatics”在线获取。
