ArticleNature protocols2021
Recovering prokaryotic genomes from host-associated, short-read shotgun metagenomic sequencing data.
Article in Nature protocols, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 42 papers, 1 of them a synthesis that pooled it.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
42 citing papers in PubMed, 1 synthesis or guideline pooled it.
- A human gut metagenome-assembled genome catalogue spanning 41 countries supports genome-scale metabolic models.Nature microbiology · 2026Pooled it
- metaFun: An analysis pipeline for metagenomic big data with fast and unified functional searches.Gut microbes · 2026Article
- Expansion of pathogens and restoration of human skin microbiome in CD4 T-cell lymphopenia.The Journal of investigative dermatology · 2026Article
- Permissive skin microbiomes in WHIM syndrome: HPV and pathogen expansion.The Journal of investigative dermatology · 2026Article
- Large-scale estimation of bacterial and archaeal DNA prevalence in metagenomes reveals biome-specific patterns.mSystems · 2026Article
- Towards standardization in pig microbiome research based on a comprehensive twenty-year review.Animal microbiome · 2026Review
- CAMP: a modular metagenomics analysis system for integrated multistep data exploration.NAR genomics and bioinformatics · 2026Article
- Advancing Plant Microbiome Research Through Host DNA Depletion Techniques.Plant biotechnology journal · 2026Review
- Linking the microbiome to the complement system in geographic atrophy.NPJ genomic medicine · 2026Article
- Absolute quantification of prokaryotes in the microbiome by 16S rRNA qPCR or ddPCR.Nature protocols · 2025Review
- Metagenomic Applications to Herbivore Gut Microbiomes: A Comprehensive Review of Microbial Diversity and Host Interactions.Animals : an open access journal from MDPI · 2025Review
- Unveiling soil microbial diversity through ultra-deep short-read metagenomic sequencing and co-assembly.iMeta · 2025Article
- MetaflowX: a scalable and resource-efficient workflow for multi-strategy metagenomic analysis.Nucleic acids research · 2025Article
- MAGdb: a comprehensive high quality MAGs repository for exploring microbial metagenome-assemble genomes.Genome biology · 2025Article
- Plasticity of the gut microbiome of golden snub-nosed monkeys (Rhinopithecus roxellana) in response to seasonal variation in diet.NPJ biofilms and microbiomes · 2025Article
- Metagenomic profiling of gut microbime: associating their role with the advancement of diabetic nephropathy.Antonie van Leeuwenhoek · 2025Review
- Article
- Global diversity and distribution of antibiotic resistance genes in human wastewater treatment systems.Nature communications · 2025Article
- Skin microbiome and dermatologic disorders.The Journal of clinical investigation · 2025Review
- Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors.
Funding
Abstract
Recovering genomes from shotgun metagenomic sequence data allows detailed taxonomic and functional characterization of individual species or strains in a microbial community. Retrieving these metagenome-assembled genomes (MAGs) involves seven stages. First, low-quality bases, along with adapter and host sequences, are removed. Second, overlapping sequences are assembled to create longer contiguous fragments. Third, these fragments are clustered based on sequence composition and abundance. Fourth, these sequence clusters, or bins, undergo rounds of quality assessment and refinement to yield MAGs. The optional fifth stage is dereplication of MAGs to select representatives. Next, each MAG is taxonomically classified. The optional seventh stage is assessing the fraction of diversity that has been recovered. The output of this protocol is draft genomes, which can provide invaluable clues about uncultured organisms. This protocol takes ~1 week to run, depending on computational resources available, and requires prior experience with high-performance computing, shell script programming and Python.
Indexed as
Identifiers
33864056What 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.