ArticleGenome research2008
De novo bacterial genome sequencing: millions of very short reads assembled on a desktop computer.
Article in Genome research, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 300 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.
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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.
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Who cites it
300 citing papers in PubMed.
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- Probiogenomics of Leuconostoc Mesenteroides Strains F-21 and F-22 Isolated from Human Breast Milk Reveal Beneficial Properties.Probiotics and antimicrobial proteins · 2025Article
- Gut bacterium Intestinimonas butyriciproducens improves host metabolic health: evidence from cohort and animal intervention studies.Microbiome · 2025Article
- Genomic Analyses of Methicillin-Susceptible and Methicillin-ResistantPathogens (Basel, Switzerland) · 2024Article
- Comparative genetic and pathogenic approaches of Escherichia coli isolated simultaneously from pyometra and urine of bitches.Veterinary research communications · 2024Article
- Environmental Biofilms from an Urban Community in Salvador, Brazil, Shelter Previously Uncharacterized Saprophytic Leptospira.Microbial ecology · 2023Article
- Genome analysis of a coral-associated bacterial consortium highlights complementary hydrocarbon degradation ability and other beneficial mechanisms for the host.Scientific reports · 2023Article
- Genomic Characterization ofAntibiotics (Basel, Switzerland) · 2023Article
- Reference-free phylogeny from sequencing data.BioData mining · 2023Article
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- Hybrid Genomic Analysis ofMicroorganisms · 2022Article
- Independent evolution of multi-dominant viral genome species observed in a hepatitis C virus carrier.Biochemistry and biophysics reports · 2022Article
- Conventional and Omics Approaches for Understanding the Abiotic Stress Response in Cereal Crops-An Updated Overview.Plants (Basel, Switzerland) · 2022Review
- Unraveling the Genomic Potential of the Thermophilic BacteriumMicroorganisms · 2022Article
- slag: A program for seeded local assembly of genes in complex genomes.Molecular ecology resources · 2022Article
- Mitogenome-wise codon usage pattern from comparative analysis of the first mitogenome of Blepharipa sp. (Muga uzifly) with other Oestroid flies.Scientific reports · 2022Article
- Bacteriocin ProducingMicroorganisms · 2022Article
- Polyphasic Analysis Reveals Potential Petroleum Hydrocarbon Degradation and Biosurfactant Production by Rare Biosphere Thermophilic Bacteria From Deception Island, an Active Antarctic Volcano.Frontiers in microbiology · 2022Article
- The Space-Exposed Kombucha Microbial Community MemberFrontiers in microbiology · 2022Article
240 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
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Novel high-throughput DNA sequencing technologies allow researchers to characterize a bacterial genome during a single experiment and at a moderate cost. However, the increase in sequencing throughput that is allowed by using such platforms is obtained at the expense of individual sequence read length, which must be assembled into longer contigs to be exploitable. This study focuses on the Illumina sequencing platform that produces millions of very short sequences that are 35 bases in length. We propose a de novo assembler software that is dedicated to process such data. Based on a classical overlap graph representation and on the detection of potentially spurious reads, our software generates a set of accurate contigs of several kilobases that cover most of the bacterial genome. The assembly results were validated by comparing data sets that were obtained experimentally for Staphylococcus aureus strain MW2 and Helicobacter acinonychis strain Sheeba with that of their published genomes acquired by conventional sequencing of 1.5- to 3.0-kb fragments. We also provide indications that the broad coverage achieved by high-throughput sequencing might allow for the detection of clonal polymorphisms in the set of DNA molecules being sequenced.
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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.