De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis

Nature Protocols - Tập 8 Số 8 - Trang 1494-1512 - 2013
Brian J. Haas1, Alexie Papanicolaou2, Moran Yassour1, Manfred Grabherr3, Philip D. Blood4, Joshua C. Bowden5, Matthew Brian Couger6, David Eccles7, Bo Li8, Matthias Lieber9, Matthew D. MacManes10, Michael Ott2, Joshua Orvis11, Nathalie Pochet12, Francesco Strozzi13, Nathan T. Weeks14, Rick Westerman15, Thomas William16, Colin N. Dewey8, Robert Henschel17, Richard D. LeDuc17, Nir Friedman18, Aviv Regev19
1Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, Massachusetts, USA
2Commonwealth Scientific and Industrial Research Organisation (CSIRO) Ecosystem Sciences, Black Mountain Laboratories, Canberra, Australian Capital Territory, Australia
3Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
4Pittsburgh Supercomputing Center, Carnegie Mellon University, Pittsburgh, Pennsylvania, USA
5CSIRO Information Management & Technology, St. Lucia, Queensland, Australia
6Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma, USA
7Genomics Research Centre, Griffith University, Gold Coast Campus, Gold Coast, Queensland, Australia
8Department of Computer Sciences, University of Wisconsin, Madison, Wisconsin, USA
9Center for Information Services and High-performance Computing (ZIH), Technische Universität Dresden, Dresden, Germany
10California Institute for Quantitative Biosciences, University of California Berkeley, Berkeley, California, USA
11Institute for Genome Sciences, Baltimore, Maryland, USA
12Department of Plant Systems Biology, Department of Plant Biotechnology and Bioinformatics, Vlaams Instituut voor Biotechnologie (VIB), Ghent University, Ghent, Belgium
13Parco Tecnologico Padano, Località Cascina Codazza, Lodi, Italy
14United States Department of Agriculture–Agricultural Research Service, Corn Insects and Crop Genetics Research Unit, Ames, Iowa, USA
15Genomics facility, Purdue University, West Lafayette, Indiana, USA
16GWT-TUD GmbH, Saxony, Germany
17Research Technologies Division, University Information Technology Services, Indiana University, Bloomington, Indiana, USA
18The Selim and Rachel Benin School of Computer Science, The Hebrew University of Jerusalem, Jerusalem, Israel
19Department of Biology, Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA

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Nature Protocols

Tập 8 Số 8

1494-1512

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