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Next-generation sequence assembly: four stages of data processing and computational challenges

著者

Sara El-Metwally

この作品が含まれる作品: PLOS Computational Biology

出版日: 2013-12-12

main subject: DNA, biomedical investigative technique, データ処理

Cites articles 99

Date

タイトル

著者

2013-07-22

Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species

リチャード・ダービン, David Haussler, Sante Gnerre, Jay Shendure, Alexey Sergushichev, Bruno M Vieira, Keith R. Bradnam, Jason T Howard, Filipe J Ribeiro, Martin Hunt, Matthew D. MacManes, Octávio S. Paulo, Nuno A. Fonseca, Paul J. Kersey, Michael C. Schatz, Thomas D Otto, 王俊, エリック・ジャーヴィス, Binghang Liu, ダニエル・S・ロクザー, Dariusz Przybylski, Sergey Koren, Ruibang Luo, Matthias Haimel, Tak-Wah Lam, Adam Phillippy, Benedict Paten, Shaun Jackman, Guojie Zhang, Hamidreza Chitsaz, Scott J Emrich, Guillaume Chapuis, Rayan Chikhi, T Roderick Docking, Ganeshkumar Ganapathy, Dominique Lavenier, Iain Maccallum, Delphine Naquin, James Ruby, Ted Sharpe, Ian F Korf, Simone Scalabrin, Francesco Vezzi, Riccardo Vicedomini
2013-01-29

Sequence assembly demystified

Mihai Pop
2012

Optimizing hybrid assembly of next-generation sequence data from Enterococcus faecium: a microbe with highly divergent genome
2012-11-17

VAGUE: a graphical user interface for the Velvet assembler

David Powell, Torsten Seemann
2012-11-01

NGS analyses by visualization with Trackster

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2012-07-05

Comparison of next-generation sequencing systems
2012-07-24

A tale of three next generation sequencing platforms: comparison of Ion Torrent, Pacific Biosciences and Illumina MiSeq sequencers

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2012-07-16

Slim-filter: an interactive Windows-based application for illumina genome analyzer data assessment and manipulation
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Hybrid error correction and de novo assembly of single-molecule sequencing reads

エリック・ジャーヴィス, Jason T Howard, Sergey Koren, Adam Phillippy, Michael C. Schatz, Brian P Walenz, Ganeshkumar Ganapathy
2012-05-07

Exploring single-sample SNP and INDEL calling with whole-genome de novo assembly

Heng Li
2012-05-06

Readjoiner: a fast and memory efficient string graph-based sequence assembler

Giorgio Gonnella
2012-04-19

Exploiting sparseness in de novo genome assembly

Mihai Pop, Charles Harvey Cannon
2012-05-01

Performance comparison of benchtop high-throughput sequencing platforms

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2012-04-06

A survey of error-correction methods for next-generation sequencing

Srinivas Aluru
2012

Feature-by-feature--evaluating de novo sequence assembly

Francesco Vezzi
2012-03

Efficient de novo assembly of large genomes using compressed data structures

リチャード・ダービン
2012-01-06

GAGE: A critical evaluation of genome assemblies and assembly algorithms

Steven Salzberg, Mihai Pop, Sergey Koren, Adam Phillippy, Michael C. Schatz, Todd J Treangen, Aleksey V. Zimin, Arthur L. Delcher
2012-06-12

Mass spectrum sequential subtraction speeds up searching large peptide MS/MS spectra datasets against large nucleotide databases for proteogenomics

Naoyuki Sugiyama
2012-12-29

SCARPA: scaffolding reads with practical algorithms

Michael Brudno
2011-12-19

Comparison of the two major classes of assembly algorithms: overlap-layout-consensus and de-bruijn-graph

Wei Fan, Xuesong Hu
2011-10-14

Paired de bruijn graphs: a novel approach for incorporating mate pair information into genome assemblers

Pavel A. Pevzner, Mark J P Chaisson
2011-10-13

Fast scaffolding with small independent mixed integer programs

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2011

Evaluation of short read metagenomic assembly
2011-09-26

Short reads, circular genome: skimming solid sequence to construct the bighorn sheep mitochondrial genome

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2011-09-19

Opera: reconstructing optimal genomic scaffolds with high-throughput paired-end sequences
2011-09-16

Assemblathon 1: a competitive assessment of de novo short read assembly methods

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2011-09-16

Bambus 2: scaffolding metagenomes

Mihai Pop, Sergey Koren
2011

Evaluation of methods for de novo genome assembly from high-throughput sequencing reads reveals dependencies that affect the quality of the results

Isidore Rigoutsos, Laxmi Parida
2011-09-07

Next-generation transcriptome assembly
2011-08-10

Efficient counting of k-mers in DNA sequences using a bloom filter

Páll Melsted, ジョナサン・K・プリチャード
2011-07-01

Error correction of high-throughput sequencing datasets with non-uniform coverage

Pavel A. Pevzner
2011-06-02

Comparative studies of de novo assembly tools for next-generation sequencing technologies

Hong-Wen Deng, Lei Zhang

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