ArticleGenome research2008
Short read fragment assembly of bacterial genomes.
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 173 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
173 citing papers in PubMed.
- From contiguity to accuracy: Validation-centered perspectives on bacterial genome assembly.Journal of microbiology (Seoul, Korea) · 2026Review
- Investigating Possible Interspecies Communication of Plasmids Associated with Transfer of Third-Generation Cephalosporin, Quinolone, and Colistin Resistance Between Simultaneously Isolated Escherichia Coli and Klebsiella Pneumoniae.Microbiology spectrum · 2023Article
- Matchtigs: minimum plain text representation of k-mer sets.Genome biology · 2023Article
- Draft Genome Sequence of Lentilactobacillus kosonis NBRC 111893, Isolated from a Japanese Sugar-Vegetable Fermented Beverage called Kôso.Microbiology resource announcements · 2022Article
- Genome Characterization ofMicrobiology resource announcements · 2022Article
- Introduction to the principles and methods underlying the recovery of metagenome-assembled genomes from metagenomic data.MicrobiologyOpen · 2022Review
- Review
- De novo assembly, transcriptome characterization and marker discovery in Indian major carp, Labeo rohita through pyrosequencing.Genetica · 2022Article
- Breeding for Economically and Environmentally Sustainable Wheat Varieties: An Integrated Approach from Genomics to Selection.Biology · 2022Review
- Article
- Cuttlefish: fast, parallel and low-memory compaction of de Bruijn graphs from large-scale genome collections.Bioinformatics (Oxford, England) · 2021Article
- Bifrost: highly parallel construction and indexing of colored and compacted de Bruijn graphs.Genome biology · 2020Article
- Accurate determination of node and arc multiplicities in de bruijn graphs using conditional random fields.BMC bioinformatics · 2020Article
- GetOrganelle: a fast and versatile toolkit for accurate de novo assembly of organelle genomes.Genome biology · 2020Article
- Whole genome sequencing identifies an allele responsible for clear vs. turbid plaque morphology in a Mycobacteriophage.BMC microbiology · 2020Article
- Viability and Composition Validation of Commercial Probiotic Products by Selective Culturing Combined with Next-Generation Sequencing.Microorganisms · 2019Article
- Article
- Conducting metagenomic studies in microbiology and clinical research.Applied microbiology and biotechnology · 2018Review
- Single-cell metagenomics: challenges and applications.Protein & cell · 2018Review
- Gene Duplication in Pseudomonas aeruginosa Improves Growth on Adenosine.Journal of bacteriology · 2017Article
113 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
2 authors.
Funding
Abstract
In the last year, high-throughput sequencing technologies have progressed from proof-of-concept to production quality. While these methods produce high-quality reads, they have yet to produce reads comparable in length to Sanger-based sequencing. Current fragment assembly algorithms have been implemented and optimized for mate-paired Sanger-based reads, and thus do not perform well on short reads produced by short read technologies. We present a new Eulerian assembler that generates nearly optimal short read assemblies of bacterial genomes and describe an approach to assemble reads in the case of the popular hybrid protocol when short and long Sanger-based reads are combined.
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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.