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De novo assembly and analysis of RNA-seq data


We describe Trans-ABySS, a de novo short-read transcriptome assembly and analysis pipeline that addresses variation in local read densities by assembling read substrings with varying stringencies and then merging the resulting contigs before analysis. Analyzing 7.4 gigabases of 50-base-pair paired-end Illumina reads from an adult mouse liver poly(A) RNA library, we identified known, new and alternative structures in expressed transcripts, and achieved high sensitivity and specificity relative to reference-based assembly methods.

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Figure 1: Representation of transcripts and contigs across assemblies.
Figure 2: Performance comparisons between ABySS and reference-based transcriptome analysis tools.

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Funding for this work was provided in part by Genome Canada, Genome British Columbia, Michael Smith Foundation for Health Research and the Canadian Institute of Health Research (CIHR), including the CIHR Bioinformatics Training Program for Health Research. We thank S. Morrissy and G. Taylor for insightful discussions, A. He for technical assistance, A. Fejes for assistance with coverage bias calculations, and A. Tuin and N. Watkins (DNA Software) for assistance with primer design.

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Authors and Affiliations



G.R. and J.S. wrote the paper. J.S., G.R. and K.M. reviewed predictions and recommended analysis methods. G.R. coordinated analysis and validation. B.K., A.-L.P. and A.T. constructed libraries under the supervision of YJ.Z. S.L. generated biological material and performed RT-PCR validation. R.A.M. supervised sequencing activities. Y.S.B., T.C., R. Corbett, R. Chiu, M.F., M.G., J.Q.Q., R.N., H.M.O., N.T., R.V., S.K.C. and R.S. developed analysis methods and code and performed analyses. R. Corbett and R. Chiu performed comparisons with reference-based methods. S.D.J. develops and maintains ABySS and generated the ABySS assemblies. A.R. contributed algorithms and code for ABySS. M.A.M., S.J.M.J. and P.A.H. directed research. S.J.M.J. suggested analysis methods. YJ.Z. and M.H. developed the WTSS protocol. J.S. supervised activities. P.A.H. supervised validation. I.B. developed ABySS and Trans-ABySS and directed bioinformatics work.

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Correspondence to Inanc Birol.

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The authors declare no competing financial interests.

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Supplementary Figures 1–21, Supplementary Tables 1–4, Supplementary Note (PDF 2262 kb)

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Robertson, G., Schein, J., Chiu, R. et al. De novo assembly and analysis of RNA-seq data. Nat Methods 7, 909–912 (2010).

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