HoCoRT: host contamination removal tool.

ABSTRACT:

Background

Shotgun metagenome sequencing data obtained from a host environment will usually be contaminated with sequences from the host organism. Host sequences should be removed before further analysis to avoid biases, reduce downstream computational load, or ensure privacy in the case of a human host. The tools that we identified, as designed specifically to perform host contamination sequence removal, were either outdated, not maintained, or complicated to use. Consequently, we have developed HoCoRT, a fast and user-friendly tool that implements several methods for optimised host sequence removal. We have evaluated the speed and accuracy of these methods.

Results

HoCoRT is an open-source command-line tool for host contamination removal. It is designed to be easy to insta

SUBMITTER: Rumbavicius I 

PROVIDER: S-EPMC10544359 | biostudies-literature | 2023 Oct

REPOSITORIES: biostudies-literature