Literature DB >> 22898652

Next-generation sequencing data interpretation: enhancing reproducibility and accessibility.

Anton Nekrutenko1, James Taylor.   

Abstract

Areas of life sciences research that were previously distant from each other in ideology, analysis practices and toolkits, such as microbial ecology and personalized medicine, have all embraced techniques that rely on next-generation sequencing instruments. Yet the capacity to generate the data greatly outpaces our ability to analyse it. Existing sequencing technologies are more mature and accessible than the methodologies that are available for individual researchers to move, store, analyse and present data in a fashion that is transparent and reproducible. Here we discuss currently pressing issues with analysis, interpretation, reproducibility and accessibility of these data, and we present promising solutions and venture into potential future developments.

Mesh:

Year:  2012        PMID: 22898652     DOI: 10.1038/nrg3305

Source DB:  PubMed          Journal:  Nat Rev Genet        ISSN: 1471-0056            Impact factor:   53.242


  43 in total

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Authors:  J Quackenbush
Journal:  Nat Rev Genet       Date:  2001-06       Impact factor: 53.242

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Authors:  Florian Halbritter; Harsh J Vaidya; Simon R Tomlinson
Journal:  Nat Methods       Date:  2011-12-28       Impact factor: 28.547

4.  An overview of the BioExtract Server: a distributed, Web-based system for genomic analysis.

Authors:  C M Lushbough; V P Brendel
Journal:  Adv Exp Med Biol       Date:  2010       Impact factor: 2.622

Review 5.  Microarray data analysis: from disarray to consolidation and consensus.

Authors:  David B Allison; Xiangqin Cui; Grier P Page; Mahyar Sabripour
Journal:  Nat Rev Genet       Date:  2006-01       Impact factor: 53.242

6.  Coding your way out of a problem.

Authors:  Jeffrey M Perkel
Journal:  Nat Methods       Date:  2011-06-29       Impact factor: 28.547

Review 7.  RNA-Seq: a revolutionary tool for transcriptomics.

Authors:  Zhong Wang; Mark Gerstein; Michael Snyder
Journal:  Nat Rev Genet       Date:  2009-01       Impact factor: 53.242

8.  Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences.

Authors:  Jeremy Goecks; Anton Nekrutenko; James Taylor
Journal:  Genome Biol       Date:  2010-08-25       Impact factor: 13.583

9.  Mobyle: a new full web bioinformatics framework.

Authors:  Bertrand Néron; Hervé Ménager; Corinne Maufrais; Nicolas Joly; Julien Maupetit; Sébastien Letort; Sébastien Carrere; Pierre Tuffery; Catherine Letondal
Journal:  Bioinformatics       Date:  2009-08-17       Impact factor: 6.937

10.  Searching for SNPs with cloud computing.

Authors:  Ben Langmead; Michael C Schatz; Jimmy Lin; Mihai Pop; Steven L Salzberg
Journal:  Genome Biol       Date:  2009-11-20       Impact factor: 13.583

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  102 in total

1.  NetworkAnalyst for statistical, visual and network-based meta-analysis of gene expression data.

Authors:  Jianguo Xia; Erin E Gill; Robert E W Hancock
Journal:  Nat Protoc       Date:  2015-05-07       Impact factor: 13.491

2.  Ten simple rules for making research software more robust.

Authors:  Morgan Taschuk; Greg Wilson
Journal:  PLoS Comput Biol       Date:  2017-04-13       Impact factor: 4.475

Review 3.  Translating next generation sequencing to practice: opportunities and necessary steps.

Authors:  Sitharthan Kamalakaran; Vinay Varadan; Angel Janevski; Nilanjana Banerjee; David Tuck; W Richard McCombie; Nevenka Dimitrova; Lyndsay N Harris
Journal:  Mol Oncol       Date:  2013-05-15       Impact factor: 6.603

4.  Omics Pipe: a community-based framework for reproducible multi-omics data analysis.

Authors:  Kathleen M Fisch; Tobias Meißner; Louis Gioia; Jean-Christophe Ducom; Tristan M Carland; Salvatore Loguercio; Andrew I Su
Journal:  Bioinformatics       Date:  2015-01-30       Impact factor: 6.937

Review 5.  RNA-Seq: Improving Our Understanding of Retinal Biology and Disease.

Authors:  Michael H Farkas; Elizabeth D Au; Maria E Sousa; Eric A Pierce
Journal:  Cold Spring Harb Perspect Med       Date:  2015-02-26       Impact factor: 6.915

Review 6.  A Primer on Infectious Disease Bacterial Genomics.

Authors:  Tarah Lynch; Aaron Petkau; Natalie Knox; Morag Graham; Gary Van Domselaar
Journal:  Clin Microbiol Rev       Date:  2016-09-07       Impact factor: 26.132

7.  Practical Computational Reproducibility in the Life Sciences.

Authors:  Björn Grüning; John Chilton; Johannes Köster; Ryan Dale; Nicola Soranzo; Marius van den Beek; Jeremy Goecks; Rolf Backofen; Anton Nekrutenko; James Taylor
Journal:  Cell Syst       Date:  2018-06-27       Impact factor: 10.304

Review 8.  Promise of personalized omics to precision medicine.

Authors:  Rui Chen; Michael Snyder
Journal:  Wiley Interdiscip Rev Syst Biol Med       Date:  2012-11-26

9.  Creating reusable tools from scripts: the Galaxy Tool Factory.

Authors:  Ross Lazarus; Antony Kaspi; Mark Ziemann
Journal:  Bioinformatics       Date:  2012-09-28       Impact factor: 6.937

10.  BioBlend: automating pipeline analyses within Galaxy and CloudMan.

Authors:  Clare Sloggett; Nuwan Goonasekera; Enis Afgan
Journal:  Bioinformatics       Date:  2013-04-28       Impact factor: 6.937

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