ArticlePloS one2010
Read length and repeat resolution: exploring prokaryote genomes using next-generation sequencing technologies.
Article in PloS one, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed.
- De-novo assembly of 82 bacterial genomes using Nanopore sequencing and prediction of biosynthetic capacity.Scientific data · 2026Article
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- Dynamic changes in the plastid and mitochondrial genomes of the angiosperm Corydalis pauciovulata (Papaveraceae).BMC plant biology · 2024Article
- A practical guide and Galaxy workflow to avoid inter-plasmidic repeat collapse and false gene loss in Unicycler's hybrid assemblies.Microbial genomics · 2024Article
- Taxonomic Evaluation of theMicroorganisms · 2021Article
- Laboratory Stock Variants of the Archetype Silver Resistance Plasmid pMG101 Demonstrate Plasmid Fusion, Loss of Transmissibility, and Transposition of TnFrontiers in microbiology · 2021Article
- Identification and Characterization of 33Microorganisms · 2020Article
- Evaluation of strategies for the assembly of diverse bacterial genomes using MinION long-read sequencing.BMC genomics · 2019Article
- PacBio-Based Mitochondrial Genome Assembly of Leucaena trichandra (Leguminosae) and an Intrageneric Assessment of Mitochondrial RNA Editing.Genome biology and evolution · 2018Article
- Whole-Genome Characterization of Bacillus cereus Associated with Specific Disease Manifestations.Infection and immunity · 2018Article
- Comparative Genomics of Completely SequencedFrontiers in microbiology · 2018Article
- Assessing the Gene Content of the Megagenome: Sugar Pine (Pinus lambertiana).G3 (Bethesda, Md.) · 2016Article
- Whole-genome sequencing to control antimicrobial resistance.Trends in genetics : TIG · 2014Review
- Rapid single-colony whole-genome sequencing of bacterial pathogens.The Journal of antimicrobial chemotherapy · 2014Article
- Diminishing return for increased Mappability with longer sequencing reads: implications of the k-mer distributions in the human genome.BMC bioinformatics · 2014Article
- User guide for mapping-by-sequencing in Arabidopsis.Genome biology · 2013Article
- Filtering duplicate reads from 454 pyrosequencing data.Bioinformatics (Oxford, England) · 2013Article
- De novo assembly of the carrot mitochondrial genome using next generation sequencing of whole genomic DNA provides first evidence of DNA transfer into an angiosperm plastid genome.BMC plant biology · 2012Article
- The discovery approaches and detection methods of microRNAs.Molecular biology reports · 2011Review
- Landscape of next-generation sequencing technologies.Analytical chemistry · 2011Review
Corrections and comments
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundThere are a growing number of next-generation sequencing technologies. At present, the most cost-effective options also produce the shortest reads. However, even for prokaryotes, there is uncertainty concerning the utility of these technologies for the de novo assembly of complete genomes. This reflects an expectation that short reads will be unable to resolve small, but presumably abundant, repeats. METHODOLOGY/PRINCIPAL
findingsUsing a simple model of repeat assembly, we develop and test a technique that, for any read length, can estimate the occurrence of unresolvable repeats in a genome, and thus predict the number of gaps that would need to be closed to produce a complete sequence. We apply this technique to 818 prokaryote genome sequences. This provides a quantitative assessment of the relative performance of various lengths. Notably, unpaired reads of only 150nt can reconstruct approximately 50% of the analysed genomes with fewer than 96 repeat-induced gaps. Nonetheless, there is considerable variation amongst prokaryotes. Some genomes can be assembled to near contiguity using very short reads while others require much longer reads.
conclusionsGiven the diversity of prokaryote genomes, a sequencing strategy should be tailored to the organism under study. Our results will provide researchers with a practical resource to guide the selection of the appropriate read length.
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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.