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

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🔗 View Article (PMC 3875132)

Published in Nat Protoc on July 11, 2013

Authors

Brian J Haas1, Alexie Papanicolaou2, Moran Yassour1,3, Manfred Grabherr4, Philip D Blood5, Joshua Bowden6, Matthew Brian Couger7, David Eccles8, Bo Li9, Matthias Lieber10, Matthew D MacManes11, Michael Ott2, Joshua Orvis12, Nathalie Pochet1,13, Francesco Strozzi14, Nathan Weeks15, Rick Westerman16, Thomas William17, Colin N Dewey9,18, Robert Henschel19, Richard D LeDuc19, Nir Friedman3, Aviv Regev1,20

Author Affiliations

1: Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA, 02142, USA.
2: CSIRO Ecosystem Sciences, Black Mountain Labs, Canberra, ACT 2601, Australia.
3: The Selim and Rachel Benin School of Computer Science, The Hebrew University of Jerusalem, Jerusalem 91904, Israel.
4: Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden.
5: Pittsburgh Supercomputing Center, Carnegie Mellon University, Pittsburgh, PA, 15213, USA.
6: CSIRO Information Management & Technology, 306 Carmody Rd, St Lucia QLD 4067, Australia.
7: Department of Microbiology and Molecular Genetics, Oklahoma State University, USA.
8: Genomics Research Centre, Griffith University, Gold Coast Campus, Qld 4222, Australia.
9: Department of Computer Sciences, University of Wisconsin, Madison, WI, 53706, USA.
10: Technische Universität Dresden, Dresden, Saxony 01062, Germany.
11: University of California, Berkeley and California Institute for Quantitative Biosciences Berkeley, CA 94720, USA.
12: Institute for Genome Sciences, Baltimore, MD, 21201, USA.
13: Department of Plant Systems Biology, VIB, Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent B-9052, Belgium.
14: Parco Tecnologico Padano, Loc. Cascina Codazza, 26900 Lodi, Italy.
15: Corn Insects and Crop Genetics Research Unit, United States Department of Agriculture--Agricultural Research Service, Ames, IA 50011, USA.
16: Genomics facility, Purdue University, West Lafayette, IN, 47907, USA.
17: GWT-TUD GmbH, Blasewitzer Strasse 43, Dresden, Saxony 01307, Germany.
18: Department of Biostatistics and Medical Informatics, University of Wisconsin, Madison, WI 53706, USA.
19: Indiana University, 2709 East 10th Street, Bloomington, IN 47408,USA.
20: Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02140.

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