Literature DB >> 19430453

How to map billions of short reads onto genomes.

Cole Trapnell1, Steven L Salzberg.   

Abstract

Mapping the vast quantities of short sequence fragments produced by next-generation sequencing platforms is a challenge. What programs are available and how do they work?

Entities:  

Mesh：

Year:  2009        PMID： 19430453      PMCID： PMC2836519          DOI： 10.1038/nbt0509-455

Source DB:  PubMed          Journal:  Nat Biotechnol        ISSN： 1087-0156            Impact factor:   54.908


  10 in total

1.  Mapping short DNA sequencing reads and calling variants using mapping quality scores.

Authors:  Heng Li; Jue Ruan; Richard Durbin
Journal:  Genome Res       Date:  2008-08-19       Impact factor: 9.043

2.  Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing.

Authors:  Qun Pan; Ofer Shai; Leo J Lee; Brendan J Frey; Benjamin J Blencowe
Journal:  Nat Genet       Date:  2008-11-02       Impact factor: 38.330

3.  The transcriptional landscape of the yeast genome defined by RNA sequencing.

Authors:  Ugrappa Nagalakshmi; Zhong Wang; Karl Waern; Chong Shou; Debasish Raha; Mark Gerstein; Michael Snyder
Journal:  Science       Date:  2008-05-01       Impact factor: 47.728

4.  Mapping and quantifying mammalian transcriptomes by RNA-Seq.

Authors:  Ali Mortazavi; Brian A Williams; Kenneth McCue; Lorian Schaeffer; Barbara Wold
Journal:  Nat Methods       Date:  2008-05-30       Impact factor: 28.547

5.  Ultrafast and memory-efficient alignment of short DNA sequences to the human genome.

Authors:  Ben Langmead; Cole Trapnell; Mihai Pop; Steven L Salzberg
Journal:  Genome Biol       Date:  2009-03-04       Impact factor: 13.583

6.  Genome-wide mapping of in vivo protein-DNA interactions.

Authors:  David S Johnson; Ali Mortazavi; Richard M Myers; Barbara Wold
Journal:  Science       Date:  2007-05-31       Impact factor: 47.728

7.  Annotating genomes with massive-scale RNA sequencing.

Authors:  France Denoeud; Jean-Marc Aury; Corinne Da Silva; Benjamin Noel; Odile Rogier; Massimo Delledonne; Michele Morgante; Giorgio Valle; Patrick Wincker; Claude Scarpelli; Olivier Jaillon; François Artiguenave
Journal:  Genome Biol       Date:  2008-12-16       Impact factor: 13.583

8.  DNA sequencing of a cytogenetically normal acute myeloid leukaemia genome.

Authors:  Timothy J Ley; Elaine R Mardis; Li Ding; Bob Fulton; Michael D McLellan; Ken Chen; David Dooling; Brian H Dunford-Shore; Sean McGrath; Matthew Hickenbotham; Lisa Cook; Rachel Abbott; David E Larson; Dan C Koboldt; Craig Pohl; Scott Smith; Amy Hawkins; Scott Abbott; Devin Locke; Ladeana W Hillier; Tracie Miner; Lucinda Fulton; Vincent Magrini; Todd Wylie; Jarret Glasscock; Joshua Conyers; Nathan Sander; Xiaoqi Shi; John R Osborne; Patrick Minx; David Gordon; Asif Chinwalla; Yu Zhao; Rhonda E Ries; Jacqueline E Payton; Peter Westervelt; Michael H Tomasson; Mark Watson; Jack Baty; Jennifer Ivanovich; Sharon Heath; William D Shannon; Rakesh Nagarajan; Matthew J Walter; Daniel C Link; Timothy A Graubert; John F DiPersio; Richard K Wilson
Journal:  Nature       Date:  2008-11-06       Impact factor: 49.962

9.  Alternative isoform regulation in human tissue transcriptomes.

Authors:  Eric T Wang; Rickard Sandberg; Shujun Luo; Irina Khrebtukova; Lu Zhang; Christine Mayr; Stephen F Kingsmore; Gary P Schroth; Christopher B Burge
Journal:  Nature       Date:  2008-11-27       Impact factor: 49.962

10.  TopHat: discovering splice junctions with RNA-Seq.

Authors:  Cole Trapnell; Lior Pachter; Steven L Salzberg
Journal:  Bioinformatics       Date:  2009-03-16       Impact factor: 6.937
  10 in total
  100 in total

1.  Assembly of large genomes using second-generation sequencing.

Authors:  Michael C Schatz; Arthur L Delcher; Steven L Salzberg
Journal:  Genome Res       Date:  2010-05-27       Impact factor: 9.043

Review 2.  Next-generation sequencing techniques for eukaryotic microorganisms: sequencing-based solutions to biological problems.

Authors:  Minou Nowrousian
Journal:  Eukaryot Cell       Date:  2010-07-02

Review 3.  Applications of next generation sequencing in molecular ecology of non-model organisms.

Authors:  R Ekblom; J Galindo
Journal:  Heredity (Edinb)       Date:  2010-12-08       Impact factor: 3.821

4.  Adaptive seeds tame genomic sequence comparison.

Authors:  Szymon M Kiełbasa; Raymond Wan; Kengo Sato; Paul Horton; Martin C Frith
Journal:  Genome Res       Date:  2011-01-05       Impact factor: 9.043

5.  De novo assembly and analysis of RNA-seq data.

Authors:  Gordon Robertson; Jacqueline Schein; Readman Chiu; Richard Corbett; Matthew Field; Shaun D Jackman; Karen Mungall; Sam Lee; Hisanaga Mark Okada; Jenny Q Qian; Malachi Griffith; Anthony Raymond; Nina Thiessen; Timothee Cezard; Yaron S Butterfield; Richard Newsome; Simon K Chan; Rong She; Richard Varhol; Baljit Kamoh; Anna-Liisa Prabhu; Angela Tam; YongJun Zhao; Richard A Moore; Martin Hirst; Marco A Marra; Steven J M Jones; Pamela A Hoodless; Inanc Birol
Journal:  Nat Methods       Date:  2010-10-10       Impact factor: 28.547

6.  Count-based differential expression analysis of RNA sequencing data using R and Bioconductor.

Authors:  Simon Anders; Davis J McCarthy; Yunshun Chen; Michal Okoniewski; Gordon K Smyth; Wolfgang Huber; Mark D Robinson
Journal:  Nat Protoc       Date:  2013-08-22       Impact factor: 13.491

Review 7.  Transcriptional analysis of endocrine disruption using zebrafish and massively parallel sequencing.

Authors:  Michael E Baker; Gary Hardiman
Journal:  J Mol Endocrinol       Date:  2014-06       Impact factor: 5.098

Review 8.  The challenges of sequencing by synthesis.

Authors:  Carl W Fuller; Lyle R Middendorf; Steven A Benner; George M Church; Timothy Harris; Xiaohua Huang; Stevan B Jovanovich; John R Nelson; Jeffery A Schloss; David C Schwartz; Dmitri V Vezenov
Journal:  Nat Biotechnol       Date:  2009-11-06       Impact factor: 54.908

Review 9.  Computation for ChIP-seq and RNA-seq studies.

Authors:  Shirley Pepke; Barbara Wold; Ali Mortazavi
Journal:  Nat Methods       Date:  2009-11       Impact factor: 28.547

Review 10.  Next-generation sequencing in aging research: emerging applications, problems, pitfalls and possible solutions.

Authors:  João Pedro de Magalhães; Caleb E Finch; Georges Janssens
Journal:  Ageing Res Rev       Date:  2009-11-10       Impact factor: 10.895
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