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Library Preparation and Data Analysis Packages for Rapid Genome Sequencing

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Fungal Secondary Metabolism

Part of the book series: Methods in Molecular Biology ((MIMB,volume 944))

Abstract

High-throughput sequencing (HTS) has quickly become a valuable tool for comparative genetics and genomics and is now regularly carried out in laboratories that are not connected to large sequencing centers. Here we describe an updated version of our protocol for constructing single- and paired-end Illumina sequencing libraries, beginning with purified genomic DNA. The present protocol can also be used for “multiplexing,” i.e. the analysis of several samples in a single flowcell lane by generating “barcoded” or “indexed” Illumina sequencing libraries in a way that is independent from Illumina-supported methods. To analyze sequencing results, we suggest several independent approaches but end users should be aware that this is a quickly evolving field and that currently many alignment (or “mapping”) and counting algorithms are being developed and tested.

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Acknowledgments

We thank Mark Dasenko, Chris Sullivan, Steve Drake, Matthew Peterson, and Scott Givan at the OSU CGRB core facility for assistance with Illumina sequencing, and Chris Sullivan, Jason Cumbie, Noah Fahlgren and Henry Priest for helpful discussions and sharing code. Work in our laboratory is supported by funds from the American Cancer Society (RSG-08-030-01-CCG), the National Institutes of Health (P01GM068087 and R01GM097637), and start-up funds from the OSU Computational and Genome Biology Initiative. The authors have no conflicting interests

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Authors and Affiliations

  1. Program for Molecular and Cellular Biology, Department of Biochemistry and Biophysics, Center for Genome Research and Biocomputing (CGRB), Oregon State University, Corvallis, OR, USA

    Kyle R. Pomraning, Kristina M. Smith, Erin L. Bredeweg, Lanelle R. Connolly, Pallavi A. Phatale & Michael Freitag

Authors
  1. Kyle R. Pomraning
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  2. Kristina M. Smith
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  3. Erin L. Bredeweg
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  4. Lanelle R. Connolly
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  5. Pallavi A. Phatale
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  6. Michael Freitag
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Corresponding author

Correspondence to Michael Freitag .

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Editors and Affiliations

  1. , Dept. of Medical Microbiology & Immunolo, University of Wisconsin-Madison, Linden Drive 1550, Madison, 53706, Wisconsin, USA

    Nancy P. Keller

  2. , Dept. of Molecular Biology & Biotechnolo, University of Sheffield, Firth Court, Sheffield, S10 2TN, United Kingdom

    Geoffrey Turner

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Pomraning, K.R., Smith, K.M., Bredeweg, E.L., Connolly, L.R., Phatale, P.A., Freitag, M. (2012). Library Preparation and Data Analysis Packages for Rapid Genome Sequencing. In: Keller, N., Turner, G. (eds) Fungal Secondary Metabolism. Methods in Molecular Biology, vol 944. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-62703-122-6_1

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  • DOI: https://doi.org/10.1007/978-1-62703-122-6_1

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  • Publisher Name: Humana Press, Totowa, NJ

  • Print ISBN: 978-1-62703-121-9

  • Online ISBN: 978-1-62703-122-6

  • eBook Packages: Springer Protocols

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