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Purifying the Impure: Sequencing Metagenomes and Metatranscriptomes from Complex Animal-associated Samples

Purifying the Impure: Sequencing Metagenomes and Metatranscriptomes from Complex Animal-associated Samples

Published on: December 22, 2014

Hecatomb: an integrated software platform for viral metagenomics.

Michael J Roach^1,2,3, Sarah J Beecroft⁴, Kathie A Mihindukulasuriya^5,6

¹Flinders Accelerator for Microbiome Exploration, Flinders University, Adelaide, SA, Australia.

|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.

Keywords:

bioinformatic workflow viral metagenomics virome virus discovery

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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.