ArticleNature biotechnology2011
Full-length transcriptome assembly from RNA-Seq data without a reference genome.
Article in Nature biotechnology, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10,790 papers.
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10,790 citing papers in PubMed.
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10,730 more citing papers are in PubMed but not listed here.
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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.
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