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Related Experiment Video

Updated: Jul 15, 2025

Automated Separation of C. elegans Variably Colonized by a Bacterial Pathogen
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HoCoRT: host contamination removal tool.

Ignas Rumbavicius1, Trine B Rounge2,3, Torbjørn Rognes4,5

  • 1Centre for Bioinformatics, Department of Informatics, University of Oslo, PO Box 1080 Blindern, 0316, Oslo, Norway.

BMC Bioinformatics
|October 2, 2023
PubMed
Summary
This summary is machine-generated.

HoCoRT is a new tool that efficiently removes host contamination from shotgun metagenome data. It offers speed and accuracy, outperforming existing methods for microbiome analysis.

Keywords:
ClassificationContaminationMicrobiomeShotgun metagenomeSoftware

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • Shotgun metagenome sequencing is prone to host organism contamination.
  • Host sequence removal is crucial for accurate microbiome analysis, reducing bias and computational load.
  • Existing host removal tools are often outdated or difficult to use.

Purpose of the Study:

  • To develop HoCoRT, a fast and user-friendly tool for optimized host sequence removal from metagenomic data.
  • To evaluate the speed and accuracy of various host removal methods implemented in HoCoRT.
  • To provide recommendations for optimal host removal strategies based on read length and microbiome type.

Main Methods:

  • HoCoRT is an open-source command-line tool for host contamination removal.
  • It utilizes various mapping, classification, and alignment methods (e.g., BioBloom, Bowtie2, HISAT2, Kraken2, Minimap2).
  • Methods were evaluated using synthetic and public human gut and oral microbiome datasets with short and long reads.

Main Results:

  • HoCoRT offers a user-friendly interface with options for genome indexing and method selection.
  • For short reads, BioBloom, Bowtie2, and HISAT2 provided optimal speed/accuracy for gut microbiomes; Kraken2 was fastest but less accurate.
  • For long reads, Kraken2 and Minimap2 achieved the highest accuracy (59% human reads detected).

Conclusions:

  • HoCoRT is faster and slightly more accurate than DeconSeq for host removal.
  • Recommended optimal methods vary by read length and microbiome type.
  • HoCoRT is available as a Bioconda package with open-source code and MIT license.