ArticleBMC bioinformatics2009
Analysis and comparison of very large metagenomes with fast clustering and functional annotation.
Article in BMC bioinformatics, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 60 papers.
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Who cites it
60 citing papers in PubMed.
- Enhanced metagenomic strategies for elucidating the complexities of gut microbiota: a review.Frontiers in microbiology · 2025Review
- Assembling bacterial puzzles: piecing together functions into microbial pathways.NAR genomics and bioinformatics · 2024Article
- Analysis and Interpretation of metagenomics data: an approach.Biological procedures online · 2022Review
- Characterizing the Alteration in Rumen Microbiome and Carbohydrate-Active Enzymes Profile with Forage of Muskoxen Rumen through Comparative Metatranscriptomics.Microorganisms · 2021Article
- Comparison of Culturing and Metabarcoding Methods to Describe the Fungal Endophytic Assemblage ofBiology · 2021Article
- Novel clostridial lineages recovered from metagenomes of a hot oil reservoir.Scientific reports · 2020Article
- An Integrated Multi-Disciplinary Perspectivefor Addressing Challenges of the Human Gut Microbiome.Metabolites · 2020Review
- Article
- ANASTASIA: An Automated Metagenomic Analysis Pipeline for Novel Enzyme Discovery Exploiting Next Generation Sequencing Data.Frontiers in genetics · 2019Article
- Salinity and Time Can Alter Epibacterial Communities of an Invasive Seaweed.Frontiers in microbiology · 2019Article
- Article
- SqueezeMeta, A Highly Portable, Fully Automatic Metagenomic Analysis Pipeline.Frontiers in microbiology · 2018Article
- Exploring the Human Microbiome: The Potential Future Role of Next-Generation Sequencing in Disease Diagnosis and Treatment.Frontiers in immunology · 2018Review
- A clinician's guide to microbiome analysis.Nature reviews. Gastroenterology & hepatology · 2017Review
- Total rRNA-Seq Analysis Gives Insight into Bacterial, Fungal, Protozoal and Archaeal Communities in the Rumen Using an Optimized RNA Isolation Method.Frontiers in microbiology · 2017Article
- Automated and Accurate Estimation of Gene Family Abundance from Shotgun Metagenomes.PLoS computational biology · 2015Article
- DectICO: an alignment-free supervised metagenomic classification method based on feature extraction and dynamic selection.BMC bioinformatics · 2015Article
- Microbial Consortium Associated with the Antarctic Marine Ciliate Euplotes focardii: An Investigation from Genomic Sequences.Microbial ecology · 2015Article
- Metagenomic surveys of gut microbiota.Genomics, proteomics & bioinformatics · 2015Review
- Metatranscriptomic analysis of diminutive Thiomargarita-like bacteria ("Candidatus Thiopilula" spp.) from abyssal cold seeps of the Barbados Accretionary Prism.Applied and environmental microbiology · 2015Article
Corrections and comments
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1 author.
Funding
Abstract
backgroundThe remarkable advance of metagenomics presents significant new challenges in data analysis. Metagenomic datasets (metagenomes) are large collections of sequencing reads from anonymous species within particular environments. Computational analyses for very large metagenomes are extremely time-consuming, and there are often many novel sequences in these metagenomes that are not fully utilized. The number of available metagenomes is rapidly increasing, so fast and efficient metagenome comparison methods are in great demand.
resultsThe new metagenomic data analysis method Rapid Analysis of Multiple Metagenomes with a Clustering and Annotation Pipeline (RAMMCAP) was developed using an ultra-fast sequence clustering algorithm, fast protein family annotation tools, and a novel statistical metagenome comparison method that employs a unique graphic interface. RAMMCAP processes extremely large datasets with only moderate computational effort. It identifies raw read clusters and protein clusters that may include novel gene families, and compares metagenomes using clusters or functional annotations calculated by RAMMCAP. In this study, RAMMCAP was applied to the two largest available metagenomic collections, the "Global Ocean Sampling" and the "Metagenomic Profiling of Nine Biomes".
conclusionRAMMCAP is a very fast method that can cluster and annotate one million metagenomic reads in only hundreds of CPU hours. It is available from http://tools.camera.calit2.net/camera/rammcap/.
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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.