GenCoF: a graphical user interface to rapidly remove human genome contaminants from metagenomic datasets

• Published in: Bioinformatics (Oxford, England) Vol. 35; no. 13; pp. 2318 - 2319
• Main Authors: Czajkowski, Matthew D, Vance, Daniel P, Frese, Steven A, Casaburi, Giorgio
• Format: Journal Article
• Language: English
• Published: England Oxford University Press 01.07.2019
• Subjects: Applications Notes
• ISSN: 1367-4803; 1367-4811; 1367-4811
• 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.