ReviewBriefings in bioinformatics2020
New approaches for metagenome assembly with short reads.
Review in Briefings in bioinformatics, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 106 papers.
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
106 citing papers in PubMed.
- Sarand: exploring antimicrobial resistance gene neighbourhoods in complex metagenomic assembly graphs.NAR genomics and bioinformatics · 2026Article
- Novel Insights into Metagenomic-Assembled Genomes from Layer Chicken Housing Environment.International journal of molecular sciences · 2026Article
- Article
- Quantitative metagenomics using a portable protocol.Applied and environmental microbiology · 2026Article
- 2Pipe starts with a question: matching you with the correct pipeline for MAG reconstruction.mSystems · 2026Review
- Accurate plasmid reconstruction from metagenomics data using assembly-alignment graphs and contrastive learning.Nature biotechnology · 2026Article
- HYMET: a hybrid metagenomic pipeline for accurate and efficient taxonomic classification.GigaScience · 2026Article
- Environmental metagenomics enhances detection of circulating viruses from live poultry markets in Cambodia.Nature communications · 2026Article
- Metagenomic Assembly and Gene Prediction.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Metagenomic profiling of airborne microbial communities from aircraft filters and face masks.Microbiome · 2025Article
- High microbial diversity, functional redundancy, and prophage enrichment support the success of the yellow pencil coral,mSystems · 2025Article
- Targeted assembly recovers high ammonia monooxygenase diversity in mudflat intertides.mSystems · 2025Article
- MAGdb: a comprehensive high quality MAGs repository for exploring microbial metagenome-assemble genomes.Genome biology · 2025Article
- The crosstalk between host and rumen microbiome in cattle: insights from multi-omics approaches and genome-wide association studies.World journal of microbiology & biotechnology · 2025Review
- From air to insight: the evolution of airborne DNA sequencing technologies.Microbiology (Reading, England) · 2025Review
- Genomes of Prochlorococcus, Synechococcus, bacteria, and viruses recovered from marine picocyanobacteria cultures based on Illumina and Qitan nanopore sequencing.Scientific data · 2025Article
- Novel Gene Clusters for Secondary Metabolite Synthesis in Mesophotic Sponge-Associated Bacteria.Microbial biotechnology · 2025Article
- Whole-genome Metagenomic Sequencing Reveals Gut Microbiota Composition and Function Associated with Differential Growth Performance in Two Chicken Breeds.The journal of poultry science · 2025Article
- ARGContextProfiler: extracting and scoring the genomic contexts of antibiotic resistance genes using assembly graphs.Frontiers in microbiology · 2025Article
- Essential nucleic acid omics: a theoretical foundation for early-stage users.Frontiers in bioinformatics · 2025Review
46 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
In recent years, the use of longer range read data combined with advances in assembly algorithms has stimulated big improvements in the contiguity and quality of genome assemblies. However, these advances have not directly transferred to metagenomic data sets, as assumptions made by the single genome assembly algorithms do not apply when assembling multiple genomes at varying levels of abundance. The development of dedicated assemblers for metagenomic data was a relatively late innovation and for many years, researchers had to make do using tools designed for single genomes. This has changed in the last few years and we have seen the emergence of a new type of tool built using different principles. In this review, we describe the challenges inherent in metagenomic assemblies and compare the different approaches taken by these novel assembly tools.
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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.