ArticleGigaScience2024
Hecatomb: an integrated software platform for viral metagenomics.
Article in GigaScience, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
17 citing papers in PubMed.
- Nanopore Sequencing for Chikungunya Virus: Principles and Application.Methods in molecular biology (Clifton, N.J.) · 2027Article
- DNA sequencing for microbial surveillance in cystic fibrosis airways: advances, challenges, and clinical translation.Clinical microbiology reviews · 2026Review
- Genomic characterization of LaoThe Journal of general virology · 2026Article
- BioTester: an AI-driven automated testing framework for identifying potential quality risks in bioinformatics software.Briefings in bioinformatics · 2026Article
- Co-migration of hundreds of microbial species over metres drives selection and promotes non-motile hitchhikers.Nature communications · 2026Article
- Tools and approaches to study the human gut virome: from the bench to bioinformatics.mSystems · 2026Review
- Picobirnavirus: how do you find where it's hiding?Critical reviews in microbiology · 2026Review
- The epidermal ecotone: a proposed model system for marine viral ecology at the animal-environmental interface.NPJ biofilms and microbiomes · 2026Review
- Enhanced multi-omic viral profiling from microbial community sequencing with BAQLaVa.bioRxiv : the preprint server for biology · 2026Article
- Gut virome dynamics: from commensal to critical player in health and disease.Nature reviews. Gastroenterology & hepatology · 2026Review
- Single cell viral tagging ofGut microbes · 2025Article
- WorkflowHub: a registry for computational workflows.Scientific data · 2025Article
- MicrobiomeStatPlots: Microbiome statistics plotting gallery for meta-omics and bioinformatics.iMeta · 2025Article
- Differential microbial community assembly following co-housing versus microbiota transplant.The ISME journal · 2025Article
- Metatranscriptomic analysis of the gut virome in Muscovy ducks reveals a novel duck reovirus potentially associated with hepatic and splenic hemorrhage.Frontiers in immunology · 2025Article
- Hecatomb: an integrated software platform for viral metagenomics.GigaScience · 2024Article
- The human gut virome: composition, colonization, interactions, and impacts on human health.Frontiers in microbiology · 2023Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
11 authors.
Funding
Abstract
backgroundModern sequencing technologies offer extraordinary opportunities for virus discovery and virome analysis. Annotation of viral sequences from metagenomic data requires a complex series of steps to ensure accurate annotation of individual reads and assembled contigs. In addition, varying study designs will require project-specific statistical analyses.
findingsHere we introduce Hecatomb, a bioinformatic platform coordinating commonly used tasks required for virome analysis. Hecatomb means "a great sacrifice." In this setting, Hecatomb is "sacrificing" false-positive viral annotations using extensive quality control and tiered-database searches. Hecatomb processes metagenomic data obtained from both short- and long-read sequencing technologies, providing annotations to individual sequences and assembled contigs. Results are provided in commonly used data formats useful for downstream analysis. Here we demonstrate the functionality of Hecatomb through the reanalysis of a primate enteric and a novel coral reef virome.
conclusionHecatomb provides an integrated platform to manage many commonly used steps for virome characterization, including rigorous quality control, host removal, and both read- and contig-based analysis. Each step is managed using the Snakemake workflow manager with dependency management using Conda. Hecatomb outputs several tables properly formatted for immediate use within popular data analysis and visualization tools, enabling effective data interpretation for a variety of study designs. Hecatomb is hosted on GitHub (github.com/shandley/hecatomb) and is available for installation from Bioconda and PyPI.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.