Searching journal content for articles similar to Chaisson et al. 19 (2): 336.

Displaying results 1-10 of 15

For checked items

view abstracts
download to citation manager

Select this article
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...
OPEN ACCESS ARTICLE
Select this article
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
...to Sanger-based sequencing. Current fragment assembly algorithms have been implemented and optimized for mate-paired Sanger-based reads, and thus do not perform well on short reads produced by short read technologies. We present a new Eulerian assembler that generates nearly optimal short read assemblies...
Select this article
Resource: ECHO: A reference-free short-read error correction algorithm
- Wei-Chun Kao,
- Andrew H. Chan,
- and Yun S. Song
Genome Res. July 2011 21: 1181-1192; Published in Advance April 11, 2011, doi:10.1101/gr.111351.110
...ECHO: A reference-free short-read error correction algorithm Wei-Chun Kao 1 , Andrew H. Chan 1 and Yun S. Song 1 , 2 , 3 1Computer Science Division, University of California, Berkeley, California 94721, USA; 2Department...
Select this article
Research: Complex rearrangements and oncogene amplifications revealed by long-read DNA and RNA sequencing of a breast cancer cell line
- Maria Nattestad,
- Sara Goodwin,
- Karen Ng,
- Timour Baslan,
- Fritz J. Sedlazeck,
- Philipp Rescheneder,
- Tyler Garvin,
- Han Fang,
- James Gurtowski,
- Elizabeth Hutton,
- Elizabeth Tseng,
- Chen-Shan Chin,
- Timothy Beck,
- Yogi Sundaravadanam,
- Melissa Kramer,
- Eric Antoniou,
- John D. McPherson,
- James Hicks,
- W. Richard McCombie,
- and Michael C. Schatz
Genome Res. August 2018 28: 1126-1135; Published in Advance June 28, 2018, doi:10.1101/gr.231100.117
...-end and mate-pair sequencing to similar amounts of coverage. To investigate the relevant performance of long and short reads for cancer analysis, we perform an array of comparisons in parallel using both technologies.Read mapping and copy number analysisLong reads have more information to uniquely align...
Select this article
COMMENTARY: 2× genomes—Does depth matter?
- Phil Green
Genome Res. November 2007 17: 1547-1549; doi:10.1101/gr.7050807
..., that of the dog, to which it is ∼80% identical at the nucleotide level, and Pontius et al. (2007 , this issue) make effective use of it. In its most extreme version, assisted assembly consists simply of aligning reads to the reference , using read mate-pair information to reduce the risk of misassembly due...
OPEN ACCESS ARTICLE
Select this article
Perspective: Assembly of large genomes using second-generation sequencing
- Michael C. Schatz,
- Arthur L. Delcher,
- and Steven L. Salzberg
Genome Res. September 2010 20: 1165-1173; Published in Advance May 27, 2010, doi:10.1101/gr.101360.109
...correction methods can be very effective when coverage is deep, as it often is with newer short-read sequencing projects. The scaffolding phase of assembly focuses on resolving repeats by linking the initial contigs into scaffolds, guided by mate-pair data. Mate pairs constrain the separation distance...
Select this article
Method: Sequence-based physical mapping of complex genomes by whole genome profiling
- Jan van Oeveren,
- Marjo de Ruiter,
- Taco Jesse,
- Hein van der Poel,
- Jifeng Tang,
- Feyruz Yalcin,
- Antoine Janssen,
- Hanne Volpin,
- Keith E. Stormo,
- Robert Bogden,
- Michiel J.T. van Eijk,
- and Marcel Prins
Genome Res. April 2011 21: 618-625; Published in Advance February 1, 2011, doi:10.1101/gr.112094.110
...–1623. Cardle L, Ramsay L, Milbourne D, Macaulay M, Marshall D, Waugh R. 2000. Computational and experimental characterization of physically clustered simple sequence repeats in plants. Genetics 156: 847–854. Chaisson MJ, Brinza D, Pevzner PA. 2009. De novo fragment assembly with short mate-paired reads: Does...
Select this article
Method: TIGRA: A targeted iterative graph routing assembler for breakpoint assembly
- Ken Chen,
- Lei Chen,
- Xian Fan,
- John Wallis,
- Li Ding,
- and George Weinstock
Genome Res. February 2014 24: 310-317; Published in Advance December 4, 2013, doi:10.1101/gr.162883.113
...fragment assembly with short mate-paired reads: Does the read length matter? Genome Res 19: 336–346. Chen K,Wallis J, McLellanM, Larson D, Kalicki J, Pohl C,McGrath S,Wendl M, Zhang Q, Locke D, et al. 2009. BreakDancer: An algorithm for highresolutionmapping of genomic structural variation.NatMethods 6...
Select this article
Research: Chromothripsis during telomere crisis is independent of NHEJ, and consistent with a replicative origin
- Kez Cleal,
- Rhiannon E. Jones,
- Julia W. Grimstead,
- Eric A. Hendrickson,
- and Duncan M. Baird
Genome Res. May 2019 29: 737-749; Published in Advance March 14, 2019, doi:10.1101/gr.240705.118
...of short fragments, suggesting an opportunity to assemble SVs into contigs. Using SV-derived reads, 1101 were de novo assembled with a mean length of 579 bp and a longest contig of 2826 bp from LIG3−/−:NC3: sample 53 (Supplemental Methods). We performed Sanger sequencing of four contigs to validate...
OPEN ACCESS ARTICLE
Select this article
Next-Generation DNA Sequencing/Review: The new paradigm of flow cell sequencing
- Robert A. Holt and
- Steven J.M. Jones
Genome Res. June 2008 18: 839-846; doi:10.1101/gr.073262.107
...cell using the previously synthesized strand as template. Likewise, the ABI approach to obtaining mate-pair sequence appears to be priming a ligation series from the 5′ end of the first and then second stand of a template. The superior read lengths offered by the 454 system are a distinct advantage...

For checked items

view abstracts
download to citation manager

Searching journal content for articles similar to Chaisson et al. 19 (2): 336.

Search Results

Modify Results

This search

Preprint Server

Current Issue

In This Issue

Citation format:
Results / page:
Results order: