ArticleGenome research2002
RePS: a sequence assembler that masks exact repeats identified from the shotgun data.
Article in Genome research, 2002. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
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Who cites it
25 citing papers in PubMed.
- Global exact optimisations for chloroplast structural haplotype scaffolding.Algorithms for molecular biology : AMB · 2024Article
- Genome assembly composition of the String "ACGT" array: a review of data structure accuracy and performance challenges.PeerJ. Computer science · 2023Article
- Dissecting yield-associated loci in super hybrid rice by resequencing recombinant inbred lines and improving parental genome sequences.Proceedings of the National Academy of Sciences of the United States of America · 2013Article
- Comparative analysis of the genomes of two field isolates of the rice blast fungus Magnaporthe oryzae.PLoS genetics · 2012Article
- Evolutionary transients in the rice transcriptome.Genomics, proteomics & bioinformatics · 2010Article
- A tandem duplication of manganese superoxide dismutase in Nosema bombycis and its evolutionary origins.Journal of molecular evolution · 2010Article
- Assembly of large genomes using second-generation sequencing.Genome research · 2010Article
- A helitron-like transposon superfamily from lepidoptera disrupts (GAAA)(n) microsatellites and is responsible for flanking sequence similarity within a microsatellite family.Journal of molecular evolution · 2010Article
- De novo assembly of human genomes with massively parallel short read sequencing.Genome research · 2010Article
- The genome of the cucumber, Cucumis sativus L.Nature genetics · 2009Article
- Low-pass shotgun sequencing of the barley genome facilitates rapid identification of genes, conserved non-coding sequences and novel repeats.BMC genomics · 2008Article
- ReRep: computational detection of repetitive sequences in genome survey sequences (GSS).BMC bioinformatics · 2008Article
- From bacterial genomics to metagenomics: concept, tools and recent advances.Indian journal of microbiology · 2008Article
- A comprehensive crop genome research project: the Superhybrid Rice Genome Project in China.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2007Review
- Alternative splicing and expression profile analysis of expressed sequence tags in domestic pig.Genomics, proteomics & bioinformatics · 2007Article
- ReAS: Recovery of ancestral sequences for transposable elements from the unassembled reads of a whole genome shotgun.PLoS computational biology · 2005Article
- The Genomes of Oryza sativa: a history of duplications.PLoS biology · 2005Article
- SilkDB: a knowledgebase for silkworm biology and genomics.Nucleic acids research · 2005Article
- De novo repeat classification and fragment assembly.Genome research · 2004Article
- A comparison of rice chloroplast genomes.Plant physiology · 2004Article
Corrections and comments
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Authors and funding
22 authors.
Funding
Abstract
We describe a sequence assembler, RePS (repeat-masked Phrap with scaffolding), that explicitly identifies exact 20mer repeats from the shotgun data and removes them prior to the assembly. The established software is used to compute meaningful error probabilities for each base. Clone-end-pairing information is used to construct scaffolds that order and orient the contigs. We show with real data for human and rice that reasonable assemblies are possible even at coverages of only 4x to 6x, despite having up to 42.2% in exact repeats.
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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.