参考基因组
基因组
生物
从头转录组组装
顺序装配
转录组
计算生物学
大规模并行测序
深度测序
遗传学
RNA序列
基因
基因表达
作者
Manfred Grabherr,Brian J. Haas,Moran Yassour,Joshua Z. Levin,Dawn Thompson,Ido Amit,Xian Adiconis,Fan Lin,Raktima Raychowdhury,Qiandong Zeng,Zehua Chen,Evan Mauceli,Nir Hacohen,Andreas Gnirke,Nick Rhind,Federica Di Palma,Bruce W. Birren,Chad Nusbaum,Kerstin Lindblad‐Toh,Nir Friedman,Aviv Regev
摘要
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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