ArticleNAR genomics and bioinformatics2024
DeepMicroClass sorts metagenomic contigs into prokaryotes, eukaryotes and viruses.
Article in NAR genomics and bioinformatics, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers, 1 of them a synthesis that pooled it.
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Who cites it
17 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Bioinformatics Tools and Approaches for Virus Discovery in Genomic Data: A Systematic Review.Viruses · 2025Pooled it
- Prolonged Stagnation Reduces Treated Wastewater Biostability by Altering Microbial Community: Insights From Metaproteomics.Environmental microbiology · 2026Article
- MNBC-ME categorizes viral and plasmid sequences within metagenomes and identifies putative species or plasmid host.BMC bioinformatics · 2026Article
- De novo whole genome assembly of the globally invasive green shore crab Carcinus maenas (Linnaeus, 1758) via long-read Oxford Nanopore MinION sequencing.The Journal of heredity · 2026Article
- Diverse novel and avian-associated viruses in the ileal viromes of Northern Mockingbird (Mimus polyglottos).Archives of virology · 2026Article
- Cotton farming affects ileal virome in a sedentary wild passerine.Animal microbiome · 2026Article
- Metabarcoding and metagenomic data across aquatic environmental gradients along the coasts of France and Chile.Scientific data · 2026Article
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- Bidirectional subsethood of shared marker profiles enables accurate virus classification.Microbiome · 2025Article
- Salinity-driven shifts in estuarine viral community composition and diversity near the Shenzhen coast.Applied and environmental microbiology · 2025Article
- Tracing non-fungal eukaryotic diversity via shotgun metagenomes in the complex mudflat intertidal zones.mSystems · 2025Article
- Arctic Ocean virus communities and their seasonality, bipolarity, and prokaryotic associations.Nature communications · 2025Article
- Probing the eukaryotic microbes of ruminants with a deep-learning classifier and comprehensive protein databases.Genome research · 2025Article
- BEREN: a bioinformatic tool for recovering giant viruses, polinton-like viruses, and virophages in metagenomic data.Bioinformatics advances · 2025Article
- Article
- 4CAC: 4-class classifier of metagenome contigs using machine learning and assembly graphs.Nucleic acids research · 2024Article
Corrections and comments
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Authors and funding
8 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Sequence classification facilitates a fundamental understanding of the structure of microbial communities. Binary metagenomic sequence classifiers are insufficient because environmental metagenomes are typically derived from multiple sequence sources. Here we introduce a deep-learning based sequence classifier, DeepMicroClass, that classifies metagenomic contigs into five sequence classes, i.e. viruses infecting prokaryotic or eukaryotic hosts, eukaryotic or prokaryotic chromosomes, and prokaryotic plasmids. DeepMicroClass achieved high performance for all sequence classes at various tested sequence lengths ranging from 500 bp to 100 kbps. By benchmarking on a synthetic dataset with variable sequence class composition, we showed that DeepMicroClass obtained better performance for eukaryotic, plasmid and viral contig classification than other state-of-the-art predictors. DeepMicroClass achieved comparable performance on viral sequence classification with geNomad and VirSorter2 when benchmarked on the CAMI II marine dataset. Using a coastal daily time-series metagenomic dataset as a case study, we showed that microbial eukaryotes and prokaryotic viruses are integral to microbial communities. By analyzing monthly metagenomes collected at HOT and BATS, we found relatively higher viral read proportions in the subsurface layer in late summer, consistent with the seasonal viral infection patterns prevalent in these areas. We expect DeepMicroClass will promote metagenomic studies of under-appreciated sequence types.
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Registered trials
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