ArticleNucleic acids research2015
An ensemble strategy that significantly improves de novo assembly of microbial genomes from metagenomic next-generation sequencing data.
Article in Nucleic acids research, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 175 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
175 citing papers in PubMed.
- Comparative analysis of gut viromes in four penguin species reveals diverse novel viruses and host-associated differences.mSphere · 2026Article
- Comparison of gut viromes across captive mammals reveals extensive genetic diversity in bacteriophage dark matter and mammalian viruses.Zoological research · 2026Article
- An evaluation of computational methods for reconstruction of human viral DNA genomes.GigaScience · 2026Article
- Complete genome sequences of twoMicrobiology resource announcements · 2026Article
- Characterization of viral diversity in wild marmot blood from the Qinghai-Tibet Plateau.Frontiers in microbiology · 2026Article
- Non-parasite genome encoded virus-like RNAs reprogram the pathogenicity of human blood flukes.Nature communications · 2025Article
- Viromic analysis of cerebrospinal fluid (CSF) samples identified an unclassified RNA virus exhibiting an atypical genomic architecture.BMC microbiology · 2025Article
- Unexplored viral diversity in Siberian cranes and wild geese: metagenomic insights from a global wintering haven.mSystems · 2025Article
- Article
- Viral metagenomics reveals parvovirus dark matter of herbivorous wildlife from the Qinghai-Tibet Plateau.BMC microbiology · 2025Article
- A circovirus-like genomic sequence with unique architecture and phylogenetic relatedness to human-linked viral lineages.Frontiers in cellular and infection microbiology · 2025Article
- Viral metagenomics reveals diverse viruses in the fecal samples of children with acute respiratory infection.Frontiers in microbiology · 2025Article
- Comparison of gut viral communities between autism spectrum disorder and healthy children.Frontiers in cellular and infection microbiology · 2025Article
- Detection of Furrundu phlebovirus in Aedes scapularis (Diptera: Culicidae) collected in urban parks, in a highly urbanized city.Revista do Instituto de Medicina Tropical de Sao Paulo · 2025Article
- Unveiling the Virome of Wild Birds: Exploring CRESS-DNA Viral Dark Matter.Genome biology and evolution · 2024Article
- First Detection and Characterization ofViruses · 2024Article
- MetaAll: integrative bioinformatics workflow for analysing clinical metagenomic data.Briefings in bioinformatics · 2024Article
- Embracing Complexity: What Novel Sequencing Methods Are Teaching Us About Herpesvirus Genomic Diversity.Annual review of virology · 2024Review
- Article
- Differences between the intestinal microbial communities of healthy dogs from plateau and those of plateau dogs infected with Echinococcus.Virology journal · 2024Article
115 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
7 authors.
Funding
Abstract
Next-generation sequencing (NGS) approaches rapidly produce millions to billions of short reads, which allow pathogen detection and discovery in human clinical, animal and environmental samples. A major limitation of sequence homology-based identification for highly divergent microorganisms is the short length of reads generated by most highly parallel sequencing technologies. Short reads require a high level of sequence similarities to annotated genes to confidently predict gene function or homology. Such recognition of highly divergent homologues can be improved by reference-free (de novo) assembly of short overlapping sequence reads into larger contigs. We describe an ensemble strategy that integrates the sequential use of various de Bruijn graph and overlap-layout-consensus assemblers with a novel partitioned sub-assembly approach. We also proposed new quality metrics that are suitable for evaluating metagenome de novo assembly. We demonstrate that this new ensemble strategy tested using in silico spike-in, clinical and environmental NGS datasets achieved significantly better contigs than current approaches.
Indexed as
Identifiers
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.