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PMID: 33203859 Published · epublish English Dataset Journal Article Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, Non-P.H.S.

Highly accurate long-read HiFi sequencing data for five complex genomes.

Scientific data ·Vol. 7 ·No. 1 ·2020-00-17 ·Pages 399

Hon T, Mars K, Young G, Tsai YC, Karalius JW, Landolin JM, Maurer N, Kudrna D, Hardigan MA, Steiner CC, Knapp SJ, Ware D, Shapiro B, Peluso P, Rank DR

Abstract

The PacBio® HiFi sequencing method yields highly accurate long-read sequencing datasets with read lengths averaging 10-25 kb and accuracies greater than 99.5%. These accurate long reads can be used to improve results for complex applications such as single nucleotide and structural variant detection, genome assembly, assembly of difficult polyploid or highly repetitive genomes, and assembly of metagenomes. Currently, there is a need for sample data sets to both evaluate the benefits of these long accurate reads as well as for development of bioinformatic tools including genome assemblers, variant callers, and haplotyping algorithms. We present deep coverage HiFi datasets for five complex samples including the two inbred model genomes Mus musculus and Zea mays, as well as two complex genomes, octoploid Fragaria × ananassa and the diploid anuran Rana muscosa. Additionally, we release sequence data from a mock metagenome community. The datasets reported here can be used without restriction to develop new algorithms and explore complex genome structure and evolution. Data were generated on the PacBio Sequel II System.

MeSH Terms
Animals Fragaria/genetics Genome, Plant High-Throughput Nucleotide Sequencing Metagenome Mice/genetics Ranidae/genetics Sequence Analysis, DNA Zea mays/genetics
Authors & Affiliations
15 authors, click to expand affiliations / ORCID
Hon Ting
Pacific Biosciences of California Inc., 1305 O'Brien Dr., Menlo Park, CA, 94025, USA.
Mars Kristin
Pacific Biosciences of California Inc., 1305 O'Brien Dr., Menlo Park, CA, 94025, USA.
Young Greg
Pacific Biosciences of California Inc., 1305 O'Brien Dr., Menlo Park, CA, 94025, USA.
Tsai Yu-Chih ORCID
Pacific Biosciences of California Inc., 1305 O'Brien Dr., Menlo Park, CA, 94025, USA.
Karalius Joseph W ORCID
Pacific Biosciences of California Inc., 1305 O'Brien Dr., Menlo Park, CA, 94025, USA.
Landolin Jane M
Ravel Biotechnology Inc., 953 Indiana St., San Francisco, CA, 94107, USA.
Maurer Nicholas
Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA, 95064, USA.
Kudrna David
Arizona Genomics Institute and School of Plant Sciences, University of Arizona, Tucson, AZ, 85721, USA.
Hardigan Michael A
Department of Plant Sciences, University of California, Davis, One Shields Ave, Davis, CA, 95616-8571, USA.
Steiner Cynthia C
Conservation Genetics, Beckman Center for Conservation Research, San Diego Zoo Global, 15600 San Pasqual Valley Road, Escondido, CA, 92027, USA.
Knapp Steven J ORCID
Department of Plant Sciences, University of California, Davis, One Shields Ave, Davis, CA, 95616-8571, USA.
Ware Doreen ORCID
Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, USA. | USDA-ARS, Plant, Soil, and Nutrition Research Unit, Ithaca, NY, 14853, USA.
Shapiro Beth ORCID
Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA, 95064, USA. | Howard Hughes Medical Institute, University of California Santa Cruz, Santa Cruz, CA, 95064, USA.
Peluso Paul
Pacific Biosciences of California Inc., 1305 O'Brien Dr., Menlo Park, CA, 94025, USA.
Rank David R ORCID
Pacific Biosciences of California Inc., 1305 O'Brien Dr., Menlo Park, CA, 94025, USA. [email protected].
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Article Info
Journal
Scientific data
Abbr.
Sci Data
ISSN
2052-4463
Published
2020-00-17
Epub
2020-00-17
Pages
399
Language
English
Region
England
NLM ID
101640192
PMCID
PMC7673114
Subset
IM
Grants
United States Department of Agriculture · National Institute of Food and Agriculture (NIFA) · 2017-51181-26833
United States Department of Agriculture · Agricultural Research Service (USDA Agricultural Research Service) · 8062-21000-041
National Science Foundation (NSF) · IOS-1744001 · International
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