HoCoRT: Host contamination removal tool

Abstract

BackgroundShotgun 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, to reduce downstream computational load, or for privacy reasons in 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 The tools that we identified as designed specifically to perform host contamination sequence removal were either outdated, not maintained or complicated to use. We have therefore created HoCoRT, a fast and user friendly tool that implements several methods for optimised host sequence removal, and evaluated the speed and accuracy of these methods. ResultsHoCoRT is an open-source command-line tool for host contamination removal. It is designed to be simple to install and use, including a one-step option for genome indexing. HoCoRT uses a range of well-known mapping, classification and alignment methods for the classification of reads. The underlying classification method to be used and its parameters are selectable by the user, enabling adaptation to different circumstances. Based on our investigation of the performance of a range of methods and parameters on artificial human gut and oral microbiomes, recommendations are provided for typical data sets with short and long reads. ConclusionsTo decontaminate a human microbiome with HoCoRT, the best combination of speed and accuracy was found with BioBloom, Bowtie2 in end-to-end mode, or HISAT2 for short reads, while BioBloom performed best for long reads. For the oral microbiome, Bowtie2 was slightly more accurate than the other two, at the expense of speed. HoCoRT using Bowtie2 in end-to-end mode was found to be much faster and slightly more accurate than the dedicated DeconSeq tool. HoCoRT is distributed as a Bioconda package. Source code and documentation are available at https://github.com/ignasrum/hocort for Linux and macOS under the MIT licence.