ArticlemSystems2022
Using AnnoTree to Get More Assignments, Faster, in DIAMOND+MEGAN Microbiome Analysis.
Article in mSystems, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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Who cites it
23 citing papers in PubMed, 42 citations in OpenAlex.
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- Discovery of a novel orthototivirus-like virus in patients with vulvovaginal candidiasis.Frontiers in cellular and infection microbiology · 2026Article
- Tracking Age-Linked Antibiotic Resistance Patterns through Building-Level Wastewater Analysis.ACS ES&T water · 2025Article
- Virome characteristics of small mammals and their associated environments in pastoral areas on the Qinghai-Tibet Plateau.NPJ biofilms and microbiomes · 2025Article
- Uncovering functional deterioration in the rhizosphere microbiome associated with post-green revolution wheat cultivars.Environmental microbiome · 2025Article
- Diversity and functional features of the root-associated bacteriome are dependent on grapevine susceptibility to Plasmopara viticola.Environmental microbiome · 2025Article
- An exploratory study on the metagenomic and proteomic characterization of hypothyroidism in the first half of pregnancy and correlation with Th1/Th2 balance.Frontiers in immunology · 2025Article
- Metagenomic analysis reveals high diversity of gut viromes in yaks (Bos grunniens) from the Qinghai-Tibet Plateau.Communications biology · 2024Article
- Host specificity and cophylogeny in the "animal-gut bacteria-phage" tripartite system.NPJ biofilms and microbiomes · 2024Article
- Genomic diversity in Paenibacillus polymyxa: unveiling distinct species groups and functional variability.BMC genomics · 2024Article
- Transcriptomics analyses reveal the key genes involved in stamen petaloid formation in Alcea rosea L.BMC plant biology · 2024Article
- Discovery of novel RNA viruses through analysis of fungi-associated next-generation sequencing data.BMC genomics · 2024Article
- Deciphering Microbial Communities and Distinct Metabolic Pathways in the Tangyin Hydrothermal Fields of Okinawa Trough through Metagenomic and Genomic Analyses.Microorganisms · 2024Article
- Novel cycloviruses identified by mining human blood metagenomic data show close relationship to those from animals.Frontiers in microbiology · 2024Article
- Gut microbiome characteristics of women with hypothyroidism during early pregnancy detected by 16S rRNA amplicon sequencing and shotgun metagenomic.Frontiers in cellular and infection microbiology · 2024Article
- Gut flora alterations among aquatic fireflyiScience · 2023Article
- Microbial communities related to the sulfur cycle in the Sansha Yongle Blue Hole.Microbiology spectrum · 2023Article
- Comparative Functional Genome Analysis Reveals the Habitat Adaptation and Biocontrol Characteristics of Plant Growth-Promoting Bacteria in NCBI Databases.Microbiology spectrum · 2023Article
- Characterization of a novel papillomavirus identified from a whale (Delphinapterus leucas) pharyngeal metagenomic library.Virology journal · 2023Article
Corrections and comments
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Authors and funding
4 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
In microbiome analysis, one main approach is to align metagenomic sequencing reads against a protein reference database, such as NCBI-nr, and then to perform taxonomic and functional binning based on the alignments. This approach is embodied, for example, in the standard DIAMOND+MEGAN analysis pipeline, which first aligns reads against NCBI-nr using DIAMOND and then performs taxonomic and functional binning using MEGAN. Here, we propose the use of the AnnoTree protein database, rather than NCBI-nr, in such alignment-based analyses to determine the prokaryotic content of metagenomic samples. We demonstrate a 2-fold speedup over the usage of the prokaryotic part of NCBI-nr and increased assignment rates, in particular assigning twice as many reads to KEGG. In addition to binning to the NCBI taxonomy, MEGAN now also bins to the GTDB taxonomy.
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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.