ArticleNature communications2024
Integrating taxonomic signals from MAGs and contigs improves read annotation and taxonomic profiling of metagenomes.
Article in Nature communications, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed.
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- Deep-sea Microbial Dataset of the Antarctic Ocean (dsMDAO): A high-resolution deep-sea microbial dataset of the Antarctic Ocean reveals potential for taxonomic and functional diversity.Microbial genomics · 2026Article
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- Integrative Metagenomic Analysis Reveals Human Gut Microbiome-Derived Candidate Non-invasive Biomarkers for Type II Diabetes Mellitus.Iranian journal of medical sciences · 2026Article
- Novel Insights into Metagenomic-Assembled Genomes from Layer Chicken Housing Environment.International journal of molecular sciences · 2026Article
- Siwa spring microbiomes as reservoirs of biosynthetic gene clusters: Unlocking natural product potential.World journal of microbiology & biotechnology · 2026Article
- Prolonged Stagnation Reduces Treated Wastewater Biostability by Altering Microbial Community: Insights From Metaproteomics.Environmental microbiology · 2026Article
- Eco-evolutionary dynamics of massive, parallel bacteriophage outbreaks in compost communities.Science advances · 2026Article
- Metagenome-assembled genomes from the gut microbiome of spontaneous diabetic macaques provide insights into microbes associated with type 2 diabetes mellitus.BMC microbiology · 2026Article
- Unveiling the hidden viral biodiversity and potential ecological functions with global coral holobiont virome database.NPJ biofilms and microbiomes · 2026Article
- From individuals to communities: How genomics is transforming biodiversity conservation.Genetics and molecular biology · 2026Article
- Metabolic activity and survival strategies of thermophilic microbiomes during hyperthermophilic composting.mSystems · 2025Article
- The Role of Nucleotide Sequencing in Natural Product Drug Discovery.Journal of natural products · 2025Review
- Metagenomic approaches for studying ubiquitous yet diverse nucleoid associated proteins in microbial communities: challenges and advances.World journal of microbiology & biotechnology · 2025Review
- Computational Metagenomics: State of the Art.International journal of molecular sciences · 2025Review
- Laboratory mice engrafted with natural gut microbiota possess a wildling-like phenotype.Nature communications · 2025Article
- Article
- Discovering Hidden Archaeal and Bacterial Lipid Producers in a Euxinic Marine System.Environmental microbiology · 2025Article
- Essential nucleic acid omics: a theoretical foundation for early-stage users.Frontiers in bioinformatics · 2025Review
- SpeSpeNet: an interactive and user-friendly tool to create and explore microbial correlation networks.ISME communications · 2025Article
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7 authors.
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Abstract
Metagenomic analysis typically includes read-based taxonomic profiling, assembly, and binning of metagenome-assembled genomes (MAGs). Here we integrate these steps in Read Annotation Tool (RAT), which uses robust taxonomic signals from MAGs and contigs to enhance read annotation. RAT reconstructs taxonomic profiles with high precision and sensitivity, outperforming other state-of-the-art tools. In high-diversity groundwater samples, RAT annotates a large fraction of the metagenomic reads, calling novel taxa at the appropriate, sometimes high taxonomic ranks. Thus, RAT integrative profiling provides an accurate and comprehensive view of the microbiome from shotgun metagenomics data. The package of Contig Annotation Tool (CAT), Bin Annotation Tool (BAT), and RAT is available at https://github.com/MGXlab/CAT_pack (from CAT pack v6.0). The CAT pack now also supports Genome Taxonomy Database (GTDB) annotations.
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