Search Results - "DURBIN, RICHARD"

Efficient haplotype matching and storage using the positional Burrows–Wheeler transform (PBWT) by Durbin, Richard

“…Motivation: Over the last few years, methods based on suffix arrays using the Burrows–Wheeler Transform have been widely used for DNA sequence read matching…”
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Inference of human population history from individual whole-genome sequences by Li, Heng, Durbin, Richard

“…Human population in the genes The history of human population size is important to understanding human evolution. Heng Li and Richard Durbin use complete…”
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Revising the human mutation rate: implications for understanding human evolution by Scally, Aylwyn, Durbin, Richard

“…Recent measurements of the human mutation rate using next-generation sequencing have revealed a value of approximately half of that previously derived from…”
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Efficient de novo assembly of large genomes using compressed data structures by Simpson, Jared T, Durbin, Richard

“…De novo genome sequence assembly is important both to generate new sequence assemblies for previously uncharacterized genomes and to identify the genome…”
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Identifying and removing haplotypic duplication in primary genome assemblies by Guan, Dengfeng, McCarthy, Shane A, Wood, Jonathan, Howe, Kerstin, Wang, Yadong, Durbin, Richard

“…Abstract Motivation Rapid development in long-read sequencing and scaffolding technologies is accelerating the production of reference-quality assemblies for…”
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Mapping short DNA sequencing reads and calling variants using mapping quality scores by Li, Heng, Ruan, Jue, Durbin, Richard

“…New sequencing technologies promise a new era in the use of DNA sequence. However, some of these technologies produce very short reads, typically of a few tens…”
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BCFtools/RoH: a hidden Markov model approach for detecting autozygosity from next-generation sequencing data by Narasimhan, Vagheesh, Danecek, Petr, Scally, Aylwyn, Xue, Yali, Tyler-Smith, Chris, Durbin, Richard

“…Runs of homozygosity (RoHs) are genomic stretches of a diploid genome that show identical alleles on both chromosomes. Longer RoHs are unlikely to have arisen…”
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MitoHiFi: a python pipeline for mitochondrial genome assembly from PacBio high fidelity reads by Uliano-Silva, Marcela, Ferreira, João Gabriel R N, Krasheninnikova, Ksenia, Formenti, Giulio, Abueg, Linelle, Torrance, James, Myers, Eugene W, Durbin, Richard, Blaxter, Mark, McCarthy, Shane A

“… PacBio high fidelity (HiFi) sequencing reads are both long (15-20 kb) and highly accurate (> Q20). Because of these properties, they have revolutionised…”
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A Bayesian framework to account for complex non-genetic factors in gene expression levels greatly increases power in eQTL studies by Stegle, Oliver, Parts, Leopold, Durbin, Richard, Winn, John

“…Gene expression measurements are influenced by a wide range of factors, such as the state of the cell, experimental conditions and variants in the sequence of…”
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SNP detection and genotyping from low-coverage sequencing data on multiple diploid samples by Le, Si Quang, Durbin, Richard

“…Reductions in the cost of sequencing have enabled whole-genome sequencing to identify sequence variants segregating in a population. An efficient approach is…”
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Variation graph toolkit improves read mapping by representing genetic variation in the reference by Garrison, Erik, Sirén, Jouni, Novak, Adam M, Hickey, Glenn, Eizenga, Jordan M, Dawson, Eric T, Jones, William, Garg, Shilpa, Markello, Charles, Lin, Michael F, Paten, Benedict, Durbin, Richard

“…Reducing read mapping bias and improving complex variant detection with a highly scalable computational toolkit that implements variation graphs. Reference…”
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Haplotype-aware graph indexes by Sirén, Jouni, Garrison, Erik, Novak, Adam M, Paten, Benedict, Durbin, Richard

“…Abstract Motivation The variation graph toolkit (VG) represents genetic variation as a graph. Although each path in the graph is a potential haplotype, most…”
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The Sequence Alignment/Map format and SAMtools by Li, Heng, Handsaker, Bob, Wysoker, Alec, Fennell, Tim, Ruan, Jue, Homer, Nils, Marth, Gabor, Abecasis, Goncalo, Durbin, Richard

“…The Sequence Alignment/Map (SAM) format is a generic alignment format for storing read alignments against reference sequences, supporting short and long reads…”
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Reference-based phasing using the Haplotype Reference Consortium panel by Loh, Po-Ru, Danecek, Petr, Palamara, Pier Francesco, Fuchsberger, Christian, A Reshef, Yakir, K Finucane, Hilary, Schoenherr, Sebastian, Forer, Lukas, McCarthy, Shane, Abecasis, Goncalo R, Durbin, Richard, L Price, Alkes

“…Po-Ru Loh, Alkes Price and colleagues present Eagle2, a reference-based phasing algorithm that allows for highly accurate and efficient phasing of genotypes…”
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Sequence locally, think globally: The Darwin Tree of Life Project by Blaxter, Mark, Mieszkowska, Nova, Di Palma, Federica, Holland, Peter, Durbin, Richard, Richards, Thomas, Berriman, Matthew, Kersey, Paul, Hollingsworth, Peter, Wilson, Willie, Twyford, Alex, Gaya, Ester, Lawniczak, Mara, Lewis, Owen, Broad, Gavin, Howe, Kevin, Hart, Michelle, Flicek, Paul, Barnes, Ian

“…The goals of the Earth Biogenome Project-to sequence the genomes of all eukaryotic life on earth-are as daunting as they are ambitious. The Darwin Tree of Life…”
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Removing reference bias and improving indel calling in ancient DNA data analysis by mapping to a sequence variation graph by Martiniano, Rui, Garrison, Erik, Jones, Eppie R, Manica, Andrea, Durbin, Richard

“…During the last decade, the analysis of ancient DNA (aDNA) sequence has become a powerful tool for the study of past human populations. However, the degraded…”
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Efficient construction of an assembly string graph using the FM-index by Simpson, Jared T., Durbin, Richard

“…Motivation: Sequence assembly is a difficult problem whose importance has grown again recently as the cost of sequencing has dramatically dropped. Most new…”
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Identification of transposable element families from pangenome polymorphisms by Sierra, Pío, Durbin, Richard

“…Transposable Elements (TEs) are segments of DNA, typically a few hundred base pairs up to several tens of thousands bases long, that have the ability to…”
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The variant call format and VCFtools by Danecek, Petr, Auton, Adam, Abecasis, Goncalo, Albers, Cornelis A., Banks, Eric, DePristo, Mark A., Handsaker, Robert E., Lunter, Gerton, Marth, Gabor T., Sherry, Stephen T., McVean, Gilean, Durbin, Richard

“…The variant call format (VCF) is a generic format for storing DNA polymorphism data such as SNPs, insertions, deletions and structural variants, together with…”
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Genomic islands of speciation separate cichlid ecomorphs in an East African crater lake by Malinsky, Milan, Challis, Richard J., Tyers, Alexandra M., Schiffels, Stephan, Terai, Yohey, Ngatunga, Benjamin P., Miska, Eric A., Durbin, Richard, Genner, Martin J., Turner, George F.

“…The genomic causes and effects of divergent ecological selection during speciation are still poorly understood. Here we report the discovery and detailed…”
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