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PMID: 25977796 Published · epublish English Dataset Journal Article Research Support, U.S. Gov't, Non-P.H.S.

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

Scientific data ·Vol. 1 ·2014-00-00 ·Pages 140045

Kim KE, Peluso P, Babayan P, Yeadon PJ, Yu C, Fisher WW, Chin CS, Rapicavoli NA, Rank DR, Li J, Catcheside DE, Celniker SE, Phillippy AM, Bergman CM, Landolin JM

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.

MeSH Terms
Animals Arabidopsis/genetics Drosophila melanogaster/genetics Escherichia coli/genetics Genome, Bacterial Genome, Fungal Genome, Insect Genome, Plant Models, Animal Neurospora crassa/genetics Saccharomyces cerevisiae/genetics Sequence Analysis, DNA
Authors & Affiliations
15 authors, click to expand affiliations / ORCID
Kim Kristi E
Pacific Biosciences of California Inc. , 1380 Willow Road, Menlo Park, California 94025, USA.
Peluso Paul
Pacific Biosciences of California Inc. , 1380 Willow Road, Menlo Park, California 94025, USA.
Babayan Primo
Pacific Biosciences of California Inc. , 1380 Willow Road, Menlo Park, California 94025, USA.
Yeadon P Jane
Flinders University, School of Biological Sciences , PO Box 2100, Adelaide, South Australia 5001, Australia.
Yu Charles
Department of Genome Dynamics, Lawrence Berkeley National Laboratory, 1 Cyclotron Road , Berkeley, California 94720, USA.
Fisher William W
Department of Genome Dynamics, Lawrence Berkeley National Laboratory, 1 Cyclotron Road , Berkeley, California 94720, USA.
Chin Chen-Shan
Pacific Biosciences of California Inc. , 1380 Willow Road, Menlo Park, California 94025, USA.
Rapicavoli Nicole A
Pacific Biosciences of California Inc. , 1380 Willow Road, Menlo Park, California 94025, USA.
Rank David R
Pacific Biosciences of California Inc. , 1380 Willow Road, Menlo Park, California 94025, USA.
Li Joachim
Department of Microbiology and Immunology, UCSF , San Francisco, California 94158, USA.
Catcheside David E A
Flinders University, School of Biological Sciences , PO Box 2100, Adelaide, South Australia 5001, Australia.
Celniker Susan E
Department of Genome Dynamics, Lawrence Berkeley National Laboratory, 1 Cyclotron Road , Berkeley, California 94720, USA.
Phillippy Adam M
National Biodefense Analysis and Countermeasures Center , 110 Thomas Johnson Drive, Frederick, Maryland 21702, USA.
Bergman Casey M
Faculty of Life Sciences, University of Manchester , Oxford Road, Manchester M13 9PT, UK.
Landolin Jane M
Pacific Biosciences of California Inc. , 1380 Willow Road, Menlo Park, California 94025, USA.
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Article Info
Journal
Scientific data
Abbr.
Sci Data
ISSN
2052-4463
DOI
10.1038/sdata.2014.45
Published
2014-00-00
Epub
2014-00-25
Pages
140045
Language
English
Region
England
NLM ID
101640192
PMCID
PMC4365909
Subset
IM
External Links
PubMed source DOI: 10.1038/sdata.2014.45 PMC Full Text View journal details
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