Full-length transcriptome assembly from RNA-Seq data without a reference genome

Manfred G. Grabherr; Brian J. Haas; Moran Yassour; Joshua Z. Levin; Dawn A. Thompson; Ido Amit; Xian Adiconis; Lin Fan; Raktima Raychowdhury; Qiandong Zeng; Zehua Chen; Evan Mauceli; Nir Hacohen; Andreas Gnirke; Nicholas Rhind; Federica Di Palma; Bruce W. Birren; Chad Nusbaum; Kerstin Lindblad-Toh; Nir Friedman; Aviv Regev

doi:10.1038/nbt.1883

Full-length transcriptome assembly from RNA-Seq data without a reference genome

Manfred G. Grabherr, Brian J. Haas, Moran Yassour, Joshua Z. Levin, Dawn A. Thompson, Ido Amit, Xian Adiconis, Lin Fan, Raktima Raychowdhury, Qiandong Zeng, Zehua Chen, Evan Mauceli, Nir Hacohen, Andreas Gnirke, Nicholas Rhind, Federica Di Palma, Bruce W. Birren, Chad Nusbaum, Kerstin Lindblad-Toh, Nir Friedman^*Aviv Regev

^*Corresponding author for this work

Research output: Contribution to journal › Article › peer-review

15771 Scopus citations

Abstract

Massively parallel sequencing of cDNA has enabled deep and efficient probing of transcriptomes. Current approaches for transcript reconstruction from such data often rely on aligning reads to a reference genome, and are thus unsuitable for samples with a partial or missing reference genome. Here we present the Trinity method for de novo assembly of full-length transcripts and evaluate it on samples from fission yeast, mouse and whitefly, whose reference genome is not yet available. By efficiently constructing and analyzing sets of de Bruijn graphs, Trinity fully reconstructs a large fraction of transcripts, including alternatively spliced isoforms and transcripts from recently duplicated genes. Compared with other de novo transcriptome assemblers, Trinity recovers more full-length transcripts across a broad range of expression levels, with a sensitivity similar to methods that rely on genome alignments. Our approach provides a unified solution for transcriptome reconstruction in any sample, especially in the absence of a reference genome.

Original language	English
Pages (from-to)	644-652
Number of pages	9
Journal	Nature Biotechnology
Volume	29
Issue number	7
DOIs	https://doi.org/10.1038/nbt.1883
State	Published - Jul 2011

Bibliographical note

Funding Information:
We thank L. Gaffney for help with figure preparation, J. Bochicchio for project management, the Broad Sequencing Platform for all sequencing work, A. Papanicolaou and M. Ott for Inchworm software testing and code enhancements, and F. Ribeiro for helpful discussions regarding error pruning. The work was supported in part by a grant from the National Human Genome Research Institute (NIH 1 U54 HG03067, Lander), the Howard Hughes Medical Institute, a National Institutes of Health PIONEER award, a Burroughs Wellcome Fund–Career Award at the Scientific Interface (A.R.), the US-Israel Binational Science Foundation (N.F. and A.R.), and funds from the National Institute of Allergy and Infectious Diseases under contract no. HHSN27220090018C. M.Y. was supported by a Clore Fellowship. K.L.-T. is a recipient of the European Young Investigator Award (EYRYI) funded by the European Science Foundation. A.R. is a researcher of the Merkin Foundation for Stem Cell Research at the Broad Institute.

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Grabherr, M. G., Haas, B. J., Yassour, M., Levin, J. Z., Thompson, D. A., Amit, I., Adiconis, X., Fan, L., Raychowdhury, R., Zeng, Q., Chen, Z., Mauceli, E., Hacohen, N., Gnirke, A., Rhind, N., Di Palma, F., Birren, B. W., Nusbaum, C., Lindblad-Toh, K., ... Regev, A. (2011). Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nature Biotechnology, 29(7), 644-652. https://doi.org/10.1038/nbt.1883

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title = "Full-length transcriptome assembly from RNA-Seq data without a reference genome",

abstract = "Massively parallel sequencing of cDNA has enabled deep and efficient probing of transcriptomes. Current approaches for transcript reconstruction from such data often rely on aligning reads to a reference genome, and are thus unsuitable for samples with a partial or missing reference genome. Here we present the Trinity method for de novo assembly of full-length transcripts and evaluate it on samples from fission yeast, mouse and whitefly, whose reference genome is not yet available. By efficiently constructing and analyzing sets of de Bruijn graphs, Trinity fully reconstructs a large fraction of transcripts, including alternatively spliced isoforms and transcripts from recently duplicated genes. Compared with other de novo transcriptome assemblers, Trinity recovers more full-length transcripts across a broad range of expression levels, with a sensitivity similar to methods that rely on genome alignments. Our approach provides a unified solution for transcriptome reconstruction in any sample, especially in the absence of a reference genome.",

author = "Grabherr, {Manfred G.} and Haas, {Brian J.} and Moran Yassour and Levin, {Joshua Z.} and Thompson, {Dawn A.} and Ido Amit and Xian Adiconis and Lin Fan and Raktima Raychowdhury and Qiandong Zeng and Zehua Chen and Evan Mauceli and Nir Hacohen and Andreas Gnirke and Nicholas Rhind and {Di Palma}, Federica and Birren, {Bruce W.} and Chad Nusbaum and Kerstin Lindblad-Toh and Nir Friedman and Aviv Regev",

note = "Funding Information: We thank L. Gaffney for help with figure preparation, J. Bochicchio for project management, the Broad Sequencing Platform for all sequencing work, A. Papanicolaou and M. Ott for Inchworm software testing and code enhancements, and F. Ribeiro for helpful discussions regarding error pruning. The work was supported in part by a grant from the National Human Genome Research Institute (NIH 1 U54 HG03067, Lander), the Howard Hughes Medical Institute, a National Institutes of Health PIONEER award, a Burroughs Wellcome Fund–Career Award at the Scientific Interface (A.R.), the US-Israel Binational Science Foundation (N.F. and A.R.), and funds from the National Institute of Allergy and Infectious Diseases under contract no. HHSN27220090018C. M.Y. was supported by a Clore Fellowship. K.L.-T. is a recipient of the European Young Investigator Award (EYRYI) funded by the European Science Foundation. A.R. is a researcher of the Merkin Foundation for Stem Cell Research at the Broad Institute.",

year = "2011",

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Grabherr, MG, Haas, BJ, Yassour, M, Levin, JZ, Thompson, DA, Amit, I, Adiconis, X, Fan, L, Raychowdhury, R, Zeng, Q, Chen, Z, Mauceli, E, Hacohen, N, Gnirke, A, Rhind, N, Di Palma, F, Birren, BW, Nusbaum, C, Lindblad-Toh, K, Friedman, N & Regev, A 2011, 'Full-length transcriptome assembly from RNA-Seq data without a reference genome', Nature Biotechnology, vol. 29, no. 7, pp. 644-652. https://doi.org/10.1038/nbt.1883

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AU - Grabherr, Manfred G.

AU - Haas, Brian J.

AU - Yassour, Moran

AU - Levin, Joshua Z.

AU - Thompson, Dawn A.

AU - Amit, Ido

AU - Adiconis, Xian

AU - Fan, Lin

AU - Raychowdhury, Raktima

AU - Zeng, Qiandong

AU - Chen, Zehua

AU - Mauceli, Evan

AU - Hacohen, Nir

AU - Gnirke, Andreas

AU - Rhind, Nicholas

AU - Di Palma, Federica

AU - Birren, Bruce W.

AU - Nusbaum, Chad

AU - Lindblad-Toh, Kerstin

AU - Friedman, Nir

AU - Regev, Aviv

N1 - Funding Information: We thank L. Gaffney for help with figure preparation, J. Bochicchio for project management, the Broad Sequencing Platform for all sequencing work, A. Papanicolaou and M. Ott for Inchworm software testing and code enhancements, and F. Ribeiro for helpful discussions regarding error pruning. The work was supported in part by a grant from the National Human Genome Research Institute (NIH 1 U54 HG03067, Lander), the Howard Hughes Medical Institute, a National Institutes of Health PIONEER award, a Burroughs Wellcome Fund–Career Award at the Scientific Interface (A.R.), the US-Israel Binational Science Foundation (N.F. and A.R.), and funds from the National Institute of Allergy and Infectious Diseases under contract no. HHSN27220090018C. M.Y. was supported by a Clore Fellowship. K.L.-T. is a recipient of the European Young Investigator Award (EYRYI) funded by the European Science Foundation. A.R. is a researcher of the Merkin Foundation for Stem Cell Research at the Broad Institute.

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N2 - Massively parallel sequencing of cDNA has enabled deep and efficient probing of transcriptomes. Current approaches for transcript reconstruction from such data often rely on aligning reads to a reference genome, and are thus unsuitable for samples with a partial or missing reference genome. Here we present the Trinity method for de novo assembly of full-length transcripts and evaluate it on samples from fission yeast, mouse and whitefly, whose reference genome is not yet available. By efficiently constructing and analyzing sets of de Bruijn graphs, Trinity fully reconstructs a large fraction of transcripts, including alternatively spliced isoforms and transcripts from recently duplicated genes. Compared with other de novo transcriptome assemblers, Trinity recovers more full-length transcripts across a broad range of expression levels, with a sensitivity similar to methods that rely on genome alignments. Our approach provides a unified solution for transcriptome reconstruction in any sample, especially in the absence of a reference genome.

AB - Massively parallel sequencing of cDNA has enabled deep and efficient probing of transcriptomes. Current approaches for transcript reconstruction from such data often rely on aligning reads to a reference genome, and are thus unsuitable for samples with a partial or missing reference genome. Here we present the Trinity method for de novo assembly of full-length transcripts and evaluate it on samples from fission yeast, mouse and whitefly, whose reference genome is not yet available. By efficiently constructing and analyzing sets of de Bruijn graphs, Trinity fully reconstructs a large fraction of transcripts, including alternatively spliced isoforms and transcripts from recently duplicated genes. Compared with other de novo transcriptome assemblers, Trinity recovers more full-length transcripts across a broad range of expression levels, with a sensitivity similar to methods that rely on genome alignments. Our approach provides a unified solution for transcriptome reconstruction in any sample, especially in the absence of a reference genome.

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Full-length transcriptome assembly from RNA-Seq data without a reference genome

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