ReviewBriefings in bioinformatics2019
A review of methods and databases for metagenomic classification and assembly.
Review in Briefings in bioinformatics, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 272 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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
272 citing papers in PubMed.
- Metagenomics for antimicrobial resistance: from resistome surveillance to mechanistic inference.Journal of bacteriology · 2026Review
- Masking recurrent contaminants in reference sequences improves specificity of clinical metagenomic sequencing.Journal of clinical microbiology · 2026Article
- Profiling the Athletes' Gut Microbiome: A Critical Methodological Perspective on 16S Metabarcoding and Shotgun Metagenomics.Biology · 2026Review
- Multiple hypervariable markers improve mycobiome classification in metatranscriptome and metagenome data.Communications biology · 2026Article
- Revealing novelty from the southwestern Atlantic, Yemanjia gen. nov. and Olokunococcus gen. nov. from the coral cyanobiome of the Abrolhos Bank.Journal of phycology · 2026Article
- Fungal diversity associated with coffee leaf rust (Hemileia vastatrix) pustules based on ITS1 amplicon sequencing.World journal of microbiology & biotechnology · 2026Article
- Filtering for truth: high-precision taxonomic classification in nanopore shotgun metagenomics data through a KMA-based bioinformatic pipeline (KAPTAIN).BMC genomics · 2026Article
- Deconvolving Phylogenetic Distance Mixtures.bioRxiv : the preprint server for biology · 2026Article
- HYMET: a hybrid metagenomic pipeline for accurate and efficient taxonomic classification.GigaScience · 2026Article
- DeepTaxa: a hybrid CNN-BERT framework for 16S rRNA taxonomic classification.Bioinformatics advances · 2026Article
- Toward reproducible pig gut microbiome profiling through standardized methodologies.ISME communications · 2026Article
- Next-Gen intestinal parasite detection: Leveraging metataxonomics for improved diagnosis of intestinal protists and helminths.PloS one · 2026Article
- Advances in the detection of antimicrobial resistance in aquatic environments: a methodological perspective.Biology methods & protocols · 2026Review
- Oral Microbiome in Oral Cancer Research from Sampling to Analysis: Strategies, Challenges, and Recommendations.Cancers · 2025Review
- A high-resolution diel survey of surface ocean metagenomes, metatranscriptomes, and transfer RNA transcripts.Scientific data · 2025Article
- Detection ofFood chemistry. Molecular sciences · 2025Article
- Gene Surfing: An efficient and versatile tool for targeted enzyme mining in metagenomics.Synthetic and systems biotechnology · 2025Article
- Metagenomic Applications to Herbivore Gut Microbiomes: A Comprehensive Review of Microbial Diversity and Host Interactions.Animals : an open access journal from MDPI · 2025Review
- Deciphering the impact of contaminating microbiota in DNA extraction reagents on metagenomic next-generation sequencing workflows.Microbiology spectrum · 2025Article
- Land-use legacies shape soil microbial communities and nutrient cycling functions in rotational shifting cultivation fields of Northern Thailand.Microbial ecology · 2025Article
212 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors.
Funding
Abstract
Microbiome research has grown rapidly over the past decade, with a proliferation of new methods that seek to make sense of large, complex data sets. Here, we survey two of the primary types of methods for analyzing microbiome data: read classification and metagenomic assembly, and we review some of the challenges facing these methods. All of the methods rely on public genome databases, and we also discuss the content of these databases and how their quality has a direct impact on our ability to interpret a microbiome sample.
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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.