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Long-read, whole-genome shotgun sequence data for five model organisms

Kristi E. Kim, Paul Peluso, Primo Babayan, P. Jane Yeadon, Charles Yu, William W. Fisher, Chen-Shan Chin, Nicole Rapicavoli, David R. Rank, Joachim Li, David E. A. Catcheside, Susan E. Celniker, Adam M. Phillippy, Casey M. Bergman, Jane M. Landolin
doi: https://doi.org/10.1101/008037
Kristi E. Kim
1Pacific Biosciences of California Inc., 1380 Willow Road, Menlo Park, CA
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Paul Peluso
1Pacific Biosciences of California Inc., 1380 Willow Road, Menlo Park, CA
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Primo Babayan
1Pacific Biosciences of California Inc., 1380 Willow Road, Menlo Park, CA
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P. Jane Yeadon
2Flinders University, School of Biological Sciences, PO Box 2100, Adelaide, SA 5001, Australia
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Charles Yu
3Berkeley Drosophila Genome Center, Lawrence Berkeley National Laboratory, Berkeley, CA
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William W. Fisher
3Berkeley Drosophila Genome Center, Lawrence Berkeley National Laboratory, Berkeley, CA
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Chen-Shan Chin
1Pacific Biosciences of California Inc., 1380 Willow Road, Menlo Park, CA
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Nicole Rapicavoli
1Pacific Biosciences of California Inc., 1380 Willow Road, Menlo Park, CA
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David R. Rank
1Pacific Biosciences of California Inc., 1380 Willow Road, Menlo Park, CA
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Joachim Li
4Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA
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David E. A. Catcheside
2Flinders University, School of Biological Sciences, PO Box 2100, Adelaide, SA 5001, Australia
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Susan E. Celniker
3Berkeley Drosophila Genome Center, Lawrence Berkeley National Laboratory, Berkeley, CA
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Adam M. Phillippy
5National Biodefense Analysis and Countermeasures Center, 110 Thomas Johnson Drive, Frederick, MD 21702, USA
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Casey M. Bergman
6Faculty of Life Sciences, University of Manchester, Oxford Road, Manchester, UK M13 9PT
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Jane M. Landolin
1Pacific Biosciences of California Inc., 1380 Willow Road, Menlo Park, CA
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Abstract

Single molecule, real-time (SMRT) sequencing from Pacific Biosciences is increasingly used in many areas of biological research including de novo genome assembly, structural-variant identification, haplotype phasing, mRNA isoform discovery, and base-modification analyses. High-quality, public datasets of SMRT sequences can spur development of analytic tools that can accommodate unique characteristics of SMRT data (long read lengths, lack of GC or amplification bias, and a random error profile leading to high consensus accuracy). In this paper, we describe eight high-coverage SMRT sequence datasets from five organisms (Escherichia coli, Saccharomyces cerevisiae, Neurospora crassa, Arabidopsis thaliana, and Drosophila melanogaster) that have been publicly released to the general scientific community (NCBI Sequence Read Archive ID SRP040522). Data were generated using two sequencing chemistries (P4C2 and P5C3) on the PacBio RS II instrument. The datasets reported here can be used without restriction by the research community to generate whole-genome assemblies, test new algorithms, investigate genome structure and evolution, and identify base modifications in some of the most widely-studied model systems in biological research.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-ND 4.0 International license.
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Posted October 23, 2014.
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Long-read, whole-genome shotgun sequence data for five model organisms
Kristi E. Kim, Paul Peluso, Primo Babayan, P. Jane Yeadon, Charles Yu, William W. Fisher, Chen-Shan Chin, Nicole Rapicavoli, David R. Rank, Joachim Li, David E. A. Catcheside, Susan E. Celniker, Adam M. Phillippy, Casey M. Bergman, Jane M. Landolin
bioRxiv 008037; doi: https://doi.org/10.1101/008037
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Long-read, whole-genome shotgun sequence data for five model organisms
Kristi E. Kim, Paul Peluso, Primo Babayan, P. Jane Yeadon, Charles Yu, William W. Fisher, Chen-Shan Chin, Nicole Rapicavoli, David R. Rank, Joachim Li, David E. A. Catcheside, Susan E. Celniker, Adam M. Phillippy, Casey M. Bergman, Jane M. Landolin
bioRxiv 008037; doi: https://doi.org/10.1101/008037

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