Abstract

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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Acknowledgements

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.

Author information

Author notes

    • Timothee Cezard

    Present address: University of Edinburgh, Edinburgh, UK.

Affiliations

  1. Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, Canada.

    • Gordon Robertson
    • , Jacqueline Schein
    • , Readman Chiu
    • , Richard Corbett
    • , Matthew Field
    • , Shaun D Jackman
    • , Karen Mungall
    • , Hisanaga Mark Okada
    • , Jenny Q Qian
    • , Malachi Griffith
    • , Anthony Raymond
    • , Nina Thiessen
    • , Timothee Cezard
    • , Yaron S Butterfield
    • , Richard Newsome
    • , Simon K Chan
    • , Rong She
    • , Richard Varhol
    • , Baljit Kamoh
    • , Anna-Liisa Prabhu
    • , Angela Tam
    • , YongJun Zhao
    • , Richard A Moore
    • , Martin Hirst
    • , Marco A Marra
    • , Steven J M Jones
    •  & Inanc Birol
  2. Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, Canada.

    • Sam Lee
    •  & Pamela A Hoodless
  3. Department of Medical Genetics, University of British Columbia, Vancouver, Canada.

    • Marco A Marra
    • , Steven J M Jones
    •  & Pamela A Hoodless

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Contributions

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.

Competing interests

The authors declare no competing financial interests.

Corresponding author

Correspondence to Inanc Birol.

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DOI

https://doi.org/10.1038/nmeth.1517

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