ArticleCurrent protocols2021
DIAMOND+MEGAN: Fast and Easy Taxonomic and Functional Analysis of Short and Long Microbiome Sequences.
Article in Current protocols, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 84 papers.
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Who cites it
84 citing papers in PubMed, 154 citations in OpenAlex.
- Trial
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- Redundancy maintains microbial ecosystem functional potential despite taxonomic shifts between serpentine and nonserpentine soils.Microbial genomics · 2026Article
- The Spirogyra pratensis genome illuminates the evolution of developmental programs and spiral chloroplast biology.The Plant cell · 2026Article
- Trouble from the tiger: first detection of dengue virus in Aedes albopictus in Australia during a 2024 dengue outbreak on Masig Island.Parasites & vectors · 2026Article
- Metagenomic Analysis Reveals Viral Diversity in Phlebotomine Sand Flies from Caribbean Region in Colombia.Microorganisms · 2026Article
- Insights into demographic and cultural influences on the oral microbiome from historical Japanese dental calculus.Scientific reports · 2026Article
- Environmental contributors to bacterially dominated fermenting consortia of artisanal Mezcal.BMC microbiology · 2026Article
- Unraveling the Taxonomic Diversity and Functional Potential of the Tunisian Salterns, Abbassia and Thyna, via Integrated 16S-18S Amplicons and Shotgun Metagenomics.International journal of molecular sciences · 2026Article
- Genome assemblies of the liverwort Blasia pusilla uncover a well-defined pseudoautosomal region on homomorphic UV sex chromosomes.Genome biology · 2026Article
- Evidence for cable bacteria inhabiting deep in anoxic sediment reveals a novel ecological niche.Environmental microbiome · 2026Article
- Towards standardization in pig microbiome research based on a comprehensive twenty-year review.Animal microbiome · 2026Review
- 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
- Forage quality shapes physiological and gut microbial responses in moose (Alces alces) of Isle Royale National Park.Scientific reports · 2026Article
- Captive breeding of specialty animals represents an overlooked yet critical reservoir for spreading antibiotic resistance genes.The ISME journal · 2026Article
- ZOVER 2.0: a virome-based platform for zoonotic and vector-borne viruses.Nucleic acids research · 2026Article
- Viral metagenomics in mosquitoes as potential vectors of arboviruses in the Colombian Caribbean: characterisation of a "core" regional RNA virome.Memorias do Instituto Oswaldo Cruz · 2026Article
- Deciphering genotype and geography dependent microbiome composition and its role in disease suppression in Ashwagandha.Frontiers in microbiology · 2026Article
- Functional signatures of the gut microbiome in middle-aged regular runners: insights from a metagenomic study.Frontiers in physiology · 2026Article
24 more citing papers are in PubMed but not listed here.
Corrections and comments
- Erratum issued
- Erratum issued
Authors and funding
3 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
One main approach to computational analysis of microbiome sequences is to first align against a reference database of annotated protein sequences (NCBI-nr) and then perform taxonomic and functional binning of the sequences based on the resulting alignments. For both short and long reads (or assembled contigs), alignment is performed using DIAMOND, whereas taxonomic and functional binning, followed by inter- active exploration and analysis, is performed using MEGAN. We provide two step-by-step descriptions of this approach: © 2021 The Authors. Basic Protocol 1: Taxonomic and functional analysis of short read microbiome sequences Support Protocol 1: Preprocessing Basic Protocol 2: taxonomic and functional analysis of assembled long read microbiome sequences Support Protocol 2: Taxonomic binning and CheckM.
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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.