Nature Communications (May 2020)
Effect of sequence depth and length in long-read assembly of the maize inbred NC358
- Shujun Ou,
- Jianing Liu,
- Kapeel M. Chougule,
- Arkarachai Fungtammasan,
- Arun S. Seetharam,
- Joshua C. Stein,
- Victor Llaca,
- Nancy Manchanda,
- Amanda M. Gilbert,
- Sharon Wei,
- Chen-Shan Chin,
- David E. Hufnagel,
- Sarah Pedersen,
- Samantha J. Snodgrass,
- Kevin Fengler,
- Margaret Woodhouse,
- Brian P. Walenz,
- Sergey Koren,
- Adam M. Phillippy,
- Brett T. Hannigan,
- R. Kelly Dawe,
- Candice N. Hirsch,
- Matthew B. Hufford,
- Doreen Ware
Affiliations
- Shujun Ou
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University
- Jianing Liu
- Department of Genetics, University of Georgia
- Kapeel M. Chougule
- Cold Spring Harbor Laboratory
- Arkarachai Fungtammasan
- DNAnexus, Inc., Mountain View
- Arun S. Seetharam
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University
- Joshua C. Stein
- Cold Spring Harbor Laboratory
- Victor Llaca
- Genomics Technologies, Applied Science and Technology, Corteva Agriscience TM
- Nancy Manchanda
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University
- Amanda M. Gilbert
- Department of Agronomy and Plant Genetics, University of Minnesota
- Sharon Wei
- Cold Spring Harbor Laboratory
- Chen-Shan Chin
- DNAnexus, Inc., Mountain View
- David E. Hufnagel
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University
- Sarah Pedersen
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University
- Samantha J. Snodgrass
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University
- Kevin Fengler
- Genomics Technologies, Applied Science and Technology, Corteva Agriscience TM
- Margaret Woodhouse
- USDA ARS Corn Insects and Crop Genetics Research Unit
- Brian P. Walenz
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health
- Sergey Koren
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health
- Adam M. Phillippy
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health
- Brett T. Hannigan
- DNAnexus, Inc., Mountain View
- R. Kelly Dawe
- Department of Genetics, University of Georgia
- Candice N. Hirsch
- Department of Agronomy and Plant Genetics, University of Minnesota
- Matthew B. Hufford
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University
- Doreen Ware
- Cold Spring Harbor Laboratory
- DOI
- https://doi.org/10.1038/s41467-020-16037-7
- Journal volume & issue
-
Vol. 11,
no. 1
pp. 1 – 10
Abstract
Sequence depth and read length determine the quality of genome assembly. Here, the authors leverage a set of PacBio reads to develop guidelines for sequencing and assembly of complex plant genomes in order to allocate finite resources using maize as an example.
