Alta-Cyclic: a self-optimizing base caller for next-generation sequencing (original) (raw)

Nature Methods volume 5, pages 679–682 (2008)Cite this article

Abstract

Next-generation sequencing is limited to short read lengths and by high error rates. We systematically analyzed sources of noise in the Illumina Genome Analyzer that contribute to these high error rates and developed a base caller, Alta-Cyclic, that uses machine learning to compensate for noise factors. Alta-Cyclic substantially improved the number of accurate reads for sequencing runs up to 78 bases and reduced systematic biases, facilitating confident identification of sequence variants.

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Acknowledgements

We thank M. Rooks, E. Hodges, K. Fejes-Toth and C. Malone for help in preparing libraries. We thank M. Regulski, D. Rebolini and L. Cardone for Illumina sequencing, and T. Heywood for assistance with cluster computing. F. Chen, D. Hillman and J. Eisen (Lawrence Berkeley National Lab) provided the Tetrahymena micronuclear library. Y.E. is a Goldberg-Lindsay Fellow of the Watson School of Biological Sciences. P.P.M. is a Crick-Clay Professor. G.J.H. is an investigator of the Howard Hughes Medical Institute. This work was supported by grants from the US National Institute of Health, the National Science Foundation and the Stanley Foundation.

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Authors and Affiliations

  1. Watson School of Biological Sciences, 1 Bungtown Road, Cold Spring Harbor, New York, 11724, USA
    Yaniv Erlich, Partha P Mitra, Melissa delaBastide, W Richard McCombie & Gregory J Hannon
  2. Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, New York, 11724, USA
    Yaniv Erlich & Gregory J Hannon

Authors

  1. Yaniv Erlich
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  2. Partha P Mitra
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  3. Melissa delaBastide
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  4. W Richard McCombie
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  5. Gregory J Hannon
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Corresponding author

Correspondence toGregory J Hannon.

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Erlich, Y., Mitra, P., delaBastide, M. et al. Alta-Cyclic: a self-optimizing base caller for next-generation sequencing.Nat Methods 5, 679–682 (2008). https://doi.org/10.1038/nmeth.1230

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