Evolve BioSystems, Inc., Davis, CA, USA.
Department of Food Science and Technology, University of Nebraska, Lincoln, NE, USA.
Bioinformatics. 2019 Jul 1;35(13):2318-2319. doi: 10.1093/bioinformatics/bty963.
The removal of human genomic reads from shotgun metagenomic sequencing is a critical step in protecting subject privacy. Freely available tools addressing this issue require advanced programing knowledge or are limited by analytical time and data load due to their server-based nature. Here, we compared the most cited tools for host-DNA removal using synthetic and real metagenomic datasets. Then, we integrated the most efficient pipeline in a graphical user interface to make these tools available without command line use. This interface, GenCoF, rapidly removes human genome contaminants from metagenomic datasets. Additionally, the tool offers quality-filtering, data reduction and interactive modification of any parameter in order to customize the analysis. GenCoF offers both quality and host-associated filtering in a non-commercial, freely available tool in a local, interactive and easy-to-use interface.
GenCoF is freely available (under a GPL license) for Mac OS and Linux at https://github.com/MattCzajkowski/GenCoF.
Supplementary data are available at Bioinformatics online.
从鸟枪法宏基因组测序中去除人类基因组读数是保护受试者隐私的关键步骤。免费提供的解决此问题的工具需要高级编程知识，或者由于其基于服务器的性质，受到分析时间和数据负载的限制。在这里，我们使用合成和真实宏基因组数据集比较了最常被引用的用于宿主 DNA 去除的工具。然后，我们将最有效的管道集成到图形用户界面中，以便在不使用命令行的情况下使用这些工具。这个名为 GenCoF 的接口可以快速从宏基因组数据集中去除人类基因组污染物。此外，该工具还提供质量过滤、数据缩减以及对任何参数的交互式修改，以定制分析。GenCoF 在本地、交互式和易于使用的界面中提供非商业、免费的工具，实现了质量和与宿主相关的过滤。
GenCoF 可在 Mac OS 和 Linux 上免费（根据 GPL 许可证）使用，网址为 https://github.com/MattCzajkowski/GenCoF。
补充数据可在 Bioinformatics 在线获取。
