ArticleGenome research2010
A new strategy for genome assembly using short sequence reads and reduced representation libraries.
Article in Genome research, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed.
- Current Progress in Phased Genome Assembly from Long-Read DNA Sequencing Data.Methods in molecular biology (Clifton, N.J.) · 2025Review
- Analysis of evolution and genetic diversity of sweetpotato and its related different polyploidy wild species I. trifida using RAD-seq.BMC plant biology · 2018Article
- SNP-based genetic linkage map of tobacco (Nicotiana tabacum L.) using next-generation RAD sequencing.Journal of biological research (Thessalonike, Greece) · 2015Article
- Reconstructing ancient genomes and epigenomes.Nature reviews. Genetics · 2015Review
- Sugarcane genome sequencing by methylation filtration provides tools for genomic research in the genus Saccharum.The Plant journal : for cell and molecular biology · 2014Article
- Draft Genome Sequence of Kurthia huakuii LAM0618T, an Organic-Pollutant-Degrading Strain Isolated from Biogas Slurry.Genome announcements · 2014Article
- Generation of SNP datasets for orangutan population genomics using improved reduced-representation sequencing and direct comparisons of SNP calling algorithms.BMC genomics · 2014Article
- Levenshtein error-correcting barcodes for multiplexed DNA sequencing.BMC bioinformatics · 2013Article
- A combinatorial approach to the restriction of a mouse genome.BMC research notes · 2013Article
- Reference-guided assembly of four diverse Arabidopsis thaliana genomes.Proceedings of the National Academy of Sciences of the United States of America · 2011Article
- Multiple changes in peptide and lipid expression associated with regeneration in the nervous system of the medicinal leech.PloS one · 2011Article
- Evolution in agriculture: the application of evolutionary approaches to the management of biotic interactions in agro-ecosystems.Evolutionary applications · 2011Article
- Positional information resolves structural variations and uncovers an evolutionarily divergent genetic locus in accessions of Arabidopsis thaliana.Genome biology and evolution · 2011Article
- A strategy for direct mapping and identification of mutations by whole-genome sequencing.Genetics · 2010Article
- Challenges of sequencing human genomes.Briefings in bioinformatics · 2010Review
- Single-nucleotide polymorphism identification and genotyping inMolecular breeding : new strategies in plant improvementArticle
Corrections and comments
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Authors and funding
6 authors.
Funding
Abstract
We have developed a novel approach for using massively parallel short-read sequencing to generate fast and inexpensive de novo genomic assemblies comparable to those generated by capillary-based methods. The ultrashort (<100 base) sequences generated by this technology pose specific biological and computational challenges for de novo assembly of large genomes. To account for this, we devised a method for experimentally partitioning the genome using reduced representation (RR) libraries prior to assembly. We use two restriction enzymes independently to create a series of overlapping fragment libraries, each containing a tractable subset of the genome. Together, these libraries allow us to reassemble the entire genome without the need of a reference sequence. As proof of concept, we applied this approach to sequence and assembled the majority of the 125-Mb Drosophila melanogaster genome. We subsequently demonstrate the accuracy of our assembly method with meaningful comparisons against the current available D. melanogaster reference genome (dm3). The ease of assembly and accuracy for comparative genomics suggest that our approach will scale to future mammalian genome-sequencing efforts, saving both time and money without sacrificing quality.
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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.