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3 results on '"Come Raczy"'

1. k-SLAM: accurate and ultra-fast taxonomic classification and gene identification for large metagenomic data sets

Author

David, Ainsworth, Michael J E, Sternberg, Come, Raczy, and Sarah A, Butcher

Subjects
Liver Cirrhosis, Shiga-Toxigenic Escherichia coli, Case-Control Studies, Computational Biology, DNA Barcoding, Taxonomic, Humans, Metagenome, Reproducibility of Results, Metagenomics, Algorithms, Genome, Bacterial, Gastrointestinal Microbiome
Abstract

k-SLAM is a highly efficient algorithm for the characterization of metagenomic data. Unlike other ultra-fast metagenomic classifiers, full sequence alignment is performed allowing for gene identification and variant calling in addition to accurate taxonomic classification. A k-mer based method provides greater taxonomic accuracy than other classifiers and a three orders of magnitude speed increase over alignment based approaches. The use of alignments to find variants and genes along with their taxonomic origins enables novel strains to be characterized. k-SLAM's speed allows a full taxonomic classification and gene identification to be tractable on modern large data sets. A pseudo-assembly method is used to increase classification accuracy by up to 40% for species which have high sequence homology within their genus.

Published
2016

2. Isaac: ultra-fast whole-genome secondary analysis on Illumina sequencing platforms

Author

Kristina M. Little, Ilya Chorny, Swathi A. Kumar, Roman Petrovski, Han-Yu Chuang, Come Raczy, Arnold Liao, Semyon Kruglyak, Elliott H. Margulies, Morten Källberg, Michael Strömberg, Stephen Tanner, and Christopher T. Saunders

Subjects
Statistics and Probability, AcademicSubjects/SCI01060, GeneralLiterature_INTRODUCTORYANDSURVEY, Computer science, Sequence analysis, Pipeline (computing), Parallel computing, Bioinformatics, Biochemistry, Genome, DNA sequencing, Secondary analysis, Genetic variation, Humans, Ultra fast, Molecular Biology, Letter to the Editor, Illumina dye sequencing, Genome, Human, Genetic Variation, High-Throughput Nucleotide Sequencing, Sequence Analysis, DNA, Genome Analysis, Computer Science Applications, Computational Mathematics, Computational Theory and Mathematics, Genome alignment, Sequence Alignment, Software
Abstract

Summary: An ultrafast DNA sequence aligner (Isaac Genome Alignment Software) that takes advantage of high-memory hardware (>48 GB) and variant caller (Isaac Variant Caller) have been developed. We demonstrate that our combined pipeline (Isaac) is four to five times faster than BWA + GATK on equivalent hardware, with comparable accuracy as measured by trio conflict rates and sensitivity. We further show that Isaac is effective in the detection of disease-causing variants and can easily/economically be run on commodity hardware. Availability: Isaac has an open source license and can be obtained at https://github.com/sequencing. Contact: craczy@illumina.com Supplementary information: Supplementary data are available at Bioinformatics online.

Published
2013

3. Accurate whole human genome sequencing using reversible terminator chemistry

Author

Zoya Kingsbury, Marc Laurent, Jason Bryant, Konstantinos D. Diakoumakos, Klaus Maisinger, Louise Fraser, Jean Ernest Sohna Sohna, Adrian Horgan, Patrick Mccauley, Jane Rogers, David W. Elmore, Mark A. Osborne, Juying Yan, Mark Smith, Milan Fedurco, Gary P. Schroth, Belen Dominguez-Fernandez, Heng Li, Andrea Sabot, Suzanne Wakelin, Cindy Lawley, Carole Anastasi, David Klenerman, David George, Daniel P. Pliskin, Mohammed D. Alam, Svilen S. Tzonev, Mark T. Reed, Xiaohai Liu, Asha Boodhun, Lu Zhang, Aylwyn Scally, T. A. Huw Jones, Ugonna C. Egbujor, Tzvetana H. Kerelska, George Stefan Golda, Shankar Balasubramanian, Lukasz Szajkowski, Mitch Lok, Mitch K. Shiver, Paul McNitt, Simon Chang, Maria Q. Johnson, Gyoung-Dong Kang, Victor J. Quijano, Sarah E. Lee, Mike Zuerlein, Maria Candelaria Rogert Bacigalupo, Alan D. Kersey, Selena G. Barbour, Dirk J. Evers, Andrew C. Pike, Stephen Rawlings, Karin Fuentes Fajardo, Mirian S. Karbelashvili, Matthew E. Hurles, Sonia M. Novo, Xavier Lee, James C. Burrows, John Stephen West, Jingwen Wang, Ify C. Aniebo, Natasha R. Crake, Christian D. Haudenschild, Richard Shaw, Come Raczy, W. Scott Furey, Wu Xiaolin, Lambros L. Paraschos, Josefina M. Seoane, John W. Martin, Katya Hoschler, Raquel Maria Sanches-Kuiper, Nick J. McCooke, Colin Barnes, Johannes P. Sluis, Abass A. Bundu, John Milton, R. Keira Cheetham, Nancy F. Hansen, Clive Gavin Brown, Nigel P. Carter, Richard J. Carter, Chiara Rodighiero, Kim B. Stevens, Shujun Luo, Radhika M. Mammen, Phyllida M. Roe, Melanie Anne Smith, Bojan Obradovic, Johnny T. Ho, Jennifer A. Loch, Terena James, Harold Swerdlow, Dale Buermann, David E. Green, Steve Hurwitz, Joe W. Mullens, Ning Sizto, Frank L. Oaks, Eli Rusman, Natalie J. Rourke, Nikolai Romanov, Anthony J. Smith, Claire Bevis, Selene M. Virk, Ling Yau, Yuli Verhovsky, D. Chris Pinkard, Stephanie Vandevondele, Vincent Peter Smith, Rob C. Brown, Eric J. Spence, Joe Podhasky, Ana Chiva Rodriguez, Michael Lawrence Parkinson, Anthony Romieu, Joe S. Brennan, Rithy K. Roth, David Mark Dunstan Bailey, Roberto Rigatti, Anil Kumar, Phillip J. Black, Primo Baybayan, Saibal Banerjee, Matthew M. Hims, Arnold Liao, R. Neil Cooley, Omead Ostadan, Vincent A. Benoit, Andrew A. Brown, Silke Ruediger, Leslie J. Irving, Parul Mehta, James C. Mullikin, Klaudia Walter, John Rogers, Jonathan Mark Boutell, Alex P. Kindwall, Paula Kokko-Gonzales, Alger C. Pike, Michael J. O'Neill, Eric Vermaas, Subramanian V. Sankar, Sean Humphray, Steven W. Short, Gerardo Turcatti, Helen Bignell, Kimberley J. Gietzen, Peta E. Torrance, Narinder I. Heyer, David James Earnshaw, Kevin Hall, Martin R. Schenker, Richard Durbin, Philip A. Granieri, Tobias William Barr Ost, Iain R. Bancarz, Lea Pickering, David L. Gustafson, Peter Lundberg, Niall Anthony Gormley, John Bridgham, Andrew Osnowski, Scott M. Kirk, Mark R. Ewan, Keith W. Moon, Bee Ling Ng, Graham John Worsley, Anthony J. Cox, Olubunmi O. Dada, Gregory C. Walcott, Sergey Etchin, Irina Khrebtukova, Kevin Benson, Vicki H. Rae, Zemin Ning, Carolyn Tregidgo, Nestor Castillo, Colin P. Goddard, Taksina Newington, Denis V. Ivanov, Anastassia Spiridou, Maria Chiara E. Catenazzi, Neil Sutton, Kevin Harnish, Darren James Ellis, Lisa Murray, Geoffrey Paul Smith, Mark T. Ross, David R. Bentley, M. R. Pratt, Isabelle Rasolonjatovo, and Michael R. Flatbush

Subjects
Male, Genotype, 2 base encoding, Nigeria, Sequence assembly, Hybrid genome assembly, Genomics, Computational biology, Biology, Polymorphism, Single Nucleotide, Sensitivity and Specificity, Deep sequencing, Article, 03 medical and health sciences, 0302 clinical medicine, Consensus Sequence, Humans, Paired-end tag, 030304 developmental biology, Genetics, Whole genome sequencing, Chromosomes, Human, X, 0303 health sciences, Multidisciplinary, Genome, Human, DNA sequencing theory, Sequence Analysis, DNA, 030220 oncology & carcinogenesis
Abstract

DNA sequence information underpins genetic research, enabling discoveries of important biological or medical benefit. Sequencing projects have traditionally used long (400-800 base pair) reads, but the existence of reference sequences for the human and many other genomes makes it possible to develop new, fast approaches to re-sequencing, whereby shorter reads are compared to a reference to identify intraspecies genetic variation. Here we report an approach that generates several billion bases of accurate nucleotide sequence per experiment at low cost. Single molecules of DNA are attached to a flat surface, amplified in situ and used as templates for synthetic sequencing with fluorescent reversible terminator deoxyribonucleotides. Images of the surface are analysed to generate high-quality sequence. We demonstrate application of this approach to human genome sequencing on flow-sorted X chromosomes and then scale the approach to determine the genome sequence of a male Yoruba from Ibadan, Nigeria. We build an accurate consensus sequence from >30x average depth of paired 35-base reads. We characterize four million single-nucleotide polymorphisms and four hundred thousand structural variants, many of which were previously unknown. Our approach is effective for accurate, rapid and economical whole-genome re-sequencing and many other biomedical applications.

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