ArticleBioinformatics (Oxford, England)2024
MetaCerberus: distributed highly parallelized HMM-based processing for robust functional annotation across the tree of life.
Article in Bioinformatics (Oxford, England), 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
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Who cites it
26 citing papers in PubMed, 32 citations in OpenAlex.
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- Abundance-activity decoupling in sulfur-cycling bacteria reflects viral infection types in meromictic lakes.The ISME journal · 2026Article
- VIRE: a metagenome-derived, planetary-scale virome resource with environmental context.Nucleic acids research · 2026Article
- Protein structure-informed bacteriophage genome annotation with Phold.Nucleic acids research · 2026Article
- PopMAG: a Nextflow pipeline for population genetics analysis based on metagenome-assembled genomes.Bioinformatics advances · 2026Article
- Resolving the evolutionary duality of marine symbionts: redefining the genusISME communications · 2026Article
- Assembly and comparative analysis of the complete mitochondrial genome ofFrontiers in plant science · 2026Article
- Temperate and filamentous bacteriophages as reservoirs of bacterial virulence in stony coral tissue loss disease.Coral reefs (Online) · 2026Article
- Ecological and Functional Stratification of the Stool Microbiome Predicts Response to Immune Checkpoint Inhibitors across Cancer Types.Computational and structural biotechnology journal · 2026Article
- Soil microbial adaptation to carbon deprivation: shifts in lignocellulolytic gene profiles following long-term plant exclusion.Environmental microbiome · 2025Article
- Multi-domain temporal patterns reveal stable community membership but dynamic interactions in the coastal microbiome.Environmental microbiome · 2025Article
- Experimental phage evolution results in expanded host ranges against antibiotic resistant Klebsiella pneumoniae isolates.Nature communications · 2025Article
- High microbial diversity, functional redundancy, and prophage enrichment support the success of the yellow pencil coral,mSystems · 2025Article
- Seasonal patterns of viromes in urban aquatic environments of Manitoba.Applied and environmental microbiology · 2025Article
- New insights into the evolution and metabolism of the bacterial phylum Candidatus Acidulodesulfobacteriota through metagenomics.Environmental microbiome · 2025Article
- Unlocking the genomic repertoire of a cultivated megaphage.Npj viruses · 2025Article
- Computational function prediction of bacteria and phage proteins.Microbiology and molecular biology reviews : MMBR · 2025Review
- Metagenomes from cyanobacterial harmful algal blooms from lakes in Ohio (USA).Microbiology resource announcements · 2025Article
Corrections and comments
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Authors and funding
5 authors at 1 institution in 1 country.
Funding
Abstract
motivationMetaCerberus is a massively parallel, fast, low memory, scalable annotation tool for inference gene function across genomes to metacommunities. MetaCerberus provides an elusive HMM/HMMER-based tool at a rapid scale with low memory. It offers scalable gene elucidation to major public databases, including KEGG (KO), COGs, CAZy, FOAM, and specific databases for viruses, including VOGs and PHROGs, from single genomes to metacommunities.
resultsMetaCerberus is 1.3× as fast on a single node than eggNOG-mapper v2 on 5× less memory using an exclusively HMM/HMMER mode. In a direct comparison, MetaCerberus provides better annotation of viruses, phages, and archaeal viruses than DRAM, Prokka, or InterProScan. MetaCerberus annotates more KOs across domains when compared to DRAM, with a 186× smaller database, and with 63× less memory. MetaCerberus is fully integrated for automatic analysis of statistics and pathways using differential statistic tools (i.e. DESeq2 and edgeR), pathway enrichment (GAGE R), and pathview R. MetaCerberus provides a novel tool for unlocking the biosphere across the tree of life at scale. AVAILABILITY AND IMPLEMENTATION: MetaCerberus is written in Python and distributed under a BSD-3 license. The source code of MetaCerberus is freely available at https://github.com/raw-lab/metacerberus compatible with Python 3 and works on both Mac OS X and Linux. MetaCerberus can also be easily installed using bioconda: mamba create -n metacerberus -c bioconda -c conda-forge metacerberus.
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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.