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Hecatomb: an integrated software platform for viral metagenomics
Michael J Roach1,2,3, Sarah J Beecroft4, Kathie A Mihindukulasuriya5,6
1Flinders Accelerator for Microbiome Exploration, Flinders University, Adelaide, SA, Australia.
Gigascience
|June 4, 2024
Summary
Hecatomb is a new bioinformatics platform that streamlines virus discovery and virome analysis. It accurately annotates viral sequences from metagenomic data, reducing false positives and simplifying downstream interpretation for researchers.
Area of Science:
- Bioinformatics
- Virology
- Metagenomics
Background:
- Modern sequencing technologies enable extensive virus discovery and virome analysis.
- Accurate annotation of viral sequences from metagenomic data is complex, involving multiple steps for reads and contigs.
- Diverse study designs necessitate adaptable, project-specific statistical analyses.
Purpose of the Study:
- Introduce Hecatomb, a bioinformatics platform designed to coordinate essential virome analysis tasks.
- Hecatomb aims to improve accuracy by "sacrificing" false-positive viral annotations through quality control and tiered database searches.
- Provide a unified solution for processing and annotating viral sequences from various sequencing technologies.
Main Methods:
- Hecatomb integrates quality control, host removal, and read/contig-based analysis for virome characterization.
- The platform utilizes the Snakemake workflow manager for efficient task management and dependency handling via Conda.
- Supports both short- and long-read sequencing data, offering annotations for individual sequences and assembled contigs.
Main Results:
- Hecatomb successfully processed and annotated viral sequences from primate enteric and coral reef virome datasets.
- Generated results in standard formats compatible with popular data analysis and visualization tools.
- Demonstrated the platform's capability in accurately characterizing complex viromes.
Conclusions:
- Hecatomb offers an integrated, user-friendly platform for comprehensive virome analysis.
- Facilitates effective data interpretation across various study designs through standardized outputs.
- Hecatomb is publicly available on GitHub and installable via Bioconda and PyPI.
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