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

ABSTRACT:

Summary

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

SUBMITTER: Czajkowski MD 

PROVIDER: S-EPMC6596892 | biostudies-literature | 2019 Jul

REPOSITORIES: biostudies-literature