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Method: Sequencing Illumina libraries at high accuracy on the ONT MinION using R2C2
- Alexander Zee,
- Dori Z.Q. Deng,
- Matthew Adams,
- Kayla D. Schimke,
- Russell Corbett-Detig,
- Shelbi L. Russell,
- Xuan Zhang,
- Robert J. Schmitz,
- and Christopher Vollmers
Genome Res. November/December 2022 32: 2092-2106; Published in Advance November 9, 2022, doi:10.1101/gr.277031.122
...conversion on the throughput of the ONT MinION when sequencing short Illumina libraries, we processed the raw reads generated by both 1D and R2C2 sequencing runs. Raw read numbers for 1D and R2C2 runs generated from one ONT MinION flowcell were similar at around 11.8 million reads. However, 1D reads were...
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Method: Improved assembly of noisy long reads by k-mer validation
- Antonio Bernardo Carvalho,
- Eduardo G. Dupim,
- and Gabriel Goldstein
Genome Res. December 2016 26: 1710-1720; Published in Advance October 7, 2016, doi:10.1101/gr.209247.116
...Corresponding author: bernardo1963@gmail.com Abstract Genome assembly depends critically on read length. Two recent technologies, from Pacific Biosciences (PacBio) and Oxford Nanopore, produce read lengths &gt;20 kb, which yield de novo genome assemblies with vastly greater contiguity than those...
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Resource: Assemblathon 1: A competitive assessment of de novo short read assembly methods
- Dent Earl,
- Keith Bradnam,
- John St. John,
- Aaron Darling,
- Dawei Lin,
- Joseph Fass,
- Hung On Ken Yu,
- Vince Buffalo,
- Daniel R. Zerbino,
- Mark Diekhans,
- Ngan Nguyen,
- Pramila Nuwantha Ariyaratne,
- Wing-Kin Sung,
- Zemin Ning,
- Matthias Haimel,
- Jared T. Simpson,
- Nuno A. Fonseca,
- İnanç Birol,
- T. Roderick Docking,
- Isaac Y. Ho,
- Daniel S. Rokhsar,
- Rayan Chikhi,
- Dominique Lavenier,
- Guillaume Chapuis,
- Delphine Naquin,
- Nicolas Maillet,
- Michael C. Schatz,
- David R. Kelley,
- Adam M. Phillippy,
- Sergey Koren,
- Shiaw-Pyng Yang,
- Wei Wu,
- Wen-Chi Chou,
- Anuj Srivastava,
- Timothy I. Shaw,
- J. Graham Ruby,
- Peter Skewes-Cox,
- Miguel Betegon,
- Michelle T. Dimon,
- Victor Solovyev,
- Igor Seledtsov,
- Petr Kosarev,
- Denis Vorobyev,
- Ricardo Ramirez-Gonzalez,
- Richard Leggett,
- Dan MacLean,
- Fangfang Xia,
- Ruibang Luo,
- Zhenyu Li,
- Yinlong Xie,
- Binghang Liu,
- Sante Gnerre,
- Iain MacCallum,
- Dariusz Przybylski,
- Filipe J. Ribeiro,
- Shuangye Yin,
- Ted Sharpe,
- Giles Hall,
- Paul J. Kersey,
- Richard Durbin,
- Shaun D. Jackman,
- Jarrod A. Chapman,
- Xiaoqiu Huang,
- Joseph L. DeRisi,
- Mario Caccamo,
- Yingrui Li,
- David B. Jaffe,
- Richard E. Green,
- David Haussler,
- Ian Korf,
- and Benedict Paten
Genome Res. December 2011 21: 2224-2241; Published in Advance September 16, 2011, doi:10.1101/gr.126599.111
...). In this work we focus on the evaluation of methods for de novo assembly using low-cost ‘‘short read’’ technology, where the reads are comparatively short in length but large in number, the sequences being assembled represent a novel diploid and the nearest homologous to that being assembled is significantly...
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RESOURCE: Sequencing of natural strains of Arabidopsis thaliana with short reads
- Stephan Ossowski,
- Korbinian Schneeberger,
- Richard M. Clark,
- Christa Lanz,
- Norman Warthmann,
- and Detlef Weigel
Genome Res. December 2008 18: 2024-2033; Published in Advance September 25, 2008, doi:10.1101/gr.080200.108
...of the Illumina sequencing-by-synthesis (SBS) technology (formerly known as Solexa sequencing) to describe sequence variation. While assembling short reads of ∼40 bp for a moderately sized presents a host of computational challenges, we show that even moderate coverage is sufficient to reveal a large fraction...
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Resource: De novo assembly of human genomes with massively parallel short read sequencing
- Ruiqiang Li,
- Hongmei Zhu,
- Jue Ruan,
- Wubin Qian,
- Xiaodong Fang,
- Zhongbin Shi,
- Yingrui Li,
- Shengting Li,
- Gao Shan,
- Karsten Kristiansen,
- Songgang Li,
- Huanming Yang,
- Jian Wang,
- and Jun Wang
Genome Res. February 2010 20: 265-272; Published in Advance December 17, 2009, doi:10.1101/gr.097261.109
...,Weinstock GM, Gibbs RA. 2004. The Atlas assembly system. Genome Res 14: 721–732. Hernandez D, Francois P, Farinelli L, Osteras M, Schrenzel J. 2008. De novo bacterial sequencing: Millions of very short reads assembled on a desktop computer. Genome Res 18: 802–809. Huang X, Wang J, Aluru S, Yang SP, Hillier L...
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RESOURCE: De novo fragment assembly with short mate-paired reads: Does the read length matter?
- Mark J. Chaisson,
- Dumitru Brinza,
- and Pavel A. Pevzner
Genome Res. February 2009 19: 336-346; Published in Advance December 3, 2008, doi:10.1101/gr.079053.108
...Pevzner Dumitru Brinza Pevzner Pavel A. P.A. Pevzner M Chaisson Chaisson Brinza, Dumitru Chaisson Mark J. MarkJ Chaisson Chaisson, M.J Pevzner, P.A 10.1101/gr.079053.108 genome;gr.079053.108 1088-9051 De novo fragment assembly with short mate-paired reads: Does the read length matter? De novo fragment...
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Methods: A new strategy for genome assembly using short sequence reads and reduced representation libraries
- Andrew L. Young,
- Hatice Ozel Abaan,
- Daniel Zerbino,
- James C. Mullikin,
- Ewan Birney,
- and Elliott H. Margulies
Genome Res. February 2010 20: 249-256; doi:10.1101/gr.097956.109
..., Osteras M, Schrenzel J. 2008. De novo bacterial sequencing: Millions of very short reads assembled on a desktop computer. Genome Res 18: 802–809. Kuhn RM, Karolchik D, Zweig AS,Wang T, Smith KE, RosenbloomKR, Rhead B, Raney BJ, Pohl A, PheasantM, et al. 2009. TheUCSCGenome Browser Database: Update 2009...
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Methods: Short read fragment assembly of bacterial genomes
- Mark J. Chaisson and
- Pavel A. Pevzner
Genome Res. February 2008 18: 324-330; Published in Advance December 14, 2007, doi:10.1101/gr.7088808
...Short read fragment assembly of bacterial genomes Mark J. Chaisson 1 and Pavel A. Pevzner 2 , 3 1 Bioinformatics Program, University of California San Diego, La Jolla, California 92093, USA; 2 Department of Computer Science and Engineering...
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Method: Optimization of de novo transcriptome assembly from next-generation sequencing data
- Yann Surget-Groba and
- Juan I. Montoya-Burgos
Genome Res. October 2010 20: 1432-1440; Published in Advance August 6, 2010, doi:10.1101/gr.103846.109
...of gastrula until hatching—was sequenced with 71-bp single-end reads on the Illumina Genome Analyzer II platform. One sequencing lane was used and resulted in 9.56 million reads. Reads were first assembled using Velvet and a range of single k-mer lengths. For this stepwe kept the assembly obtained with k = 41...
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Methods: De novo assembly using low-coverage short read sequence data from the rice pathogen Pseudomonas syringae pv. oryzae
- Josephine A. Reinhardt,
- David A. Baltrus,
- Marc T. Nishimura,
- William R. Jeck,
- Corbin D. Jones,
- and Jeffery L. Dangl
Genome Res. February 2009 19: 294-305; Published in Advance November 17, 2008, doi:10.1101/gr.083311.108
...contributed equally to this work. Abstract We developed a novel approach for de novo genome assembly using only sequence data from high-throughput short read sequencing technologies. By combining data generated from 454 Life Sciences (Roche) and Illumina (formerly known as Solexa sequencing...
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