NDLI: Oxford Nanopore sequencing, hybrid error correction, and de novo assembly of a eukaryotic genome.

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Oxford Nanopore sequencing, hybrid error correction, and de novo assembly of a eukaryotic genome.

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Oxford Nanopore sequencing, hybrid error correction, and de novo assembly of a eukaryotic genome.

Content Provider	World Health Organization (WHO)-Global Index Medicus
Author	Goodwin, Sara Gurtowski, James Ethe-Sayers, Scott Deshpande, Panchajanya Schatz, Michael C. McCombie, W. Richard
Description	Country affiliation: United States Author Affiliation: Goodwin S ( Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA.); Gurtowski J ( Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA.); Ethe-Sayers S ( Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA.); Deshpande P ( Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA.); Schatz MC ( Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA.); McCombie WR ( Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA.)
Abstract	Monitoring the progress of DNA molecules through a membrane pore has been postulated as a method for sequencing DNA for several decades. Recently, a nanopore-based sequencing instrument, the Oxford Nanopore MinION, has become available, and we used this for sequencing the Saccharomyces cerevisiae genome. To make use of these data, we developed a novel open-source hybrid error correction algorithm Nanocorr specifically for Oxford Nanopore reads, because existing packages were incapable of assembling the long read lengths (5-50 kbp) at such high error rates (between â¼5% and 40% error). With this new method, we were able to perform a hybrid error correction of the nanopore reads using complementary MiSeq data and produce a de novo assembly that is highly contiguous and accurate: The contig N50 length is more than ten times greater than an Illumina-only assembly (678 kb versus 59.9 kbp) and has >99.88% consensus identity when compared to the reference. Furthermore, the assembly with the long nanopore reads presents a much more complete representation of the features of the genome and correctly assembles gene cassettes, rRNAs, transposable elements, and other genomic features that were almost entirely absent in the Illumina-only assembly.
File Format	HTM / HTML
ISSN	10889051
e-ISSN	15495469
DOI	10.1101/gr.191395.115
Journal	Genome Research
Issue Number	11
Volume Number	25
Language	English
Publisher	Cold Spring Harbor Laboratory Press
Publisher Date	2015-11-01
Publisher Place	United States
Access Restriction	Open
Subject Keyword	Discipline Genetics Discipline Genomics Dna, Fungal Isolation & Purification Nanopores Saccharomyces Cerevisiae Genetics Sequence Analysis, Dna Dna Transposable Elements Escherichia Coli Genomics Sequence Alignment Research Support, N.i.h., Extramural Research Support, Non-u.s. Gov't Research Support, U.s. Gov't, Non-p.h.s.
Content Type	Text
Resource Type	Article
Subject	Genetics Genetics (clinical)

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1	Ministry of Education (GoI), Department of Higher Education	Sanctioning Authority	https://www.education.gov.in/ict-initiatives
2	Indian Institute of Technology Kharagpur	Host Institute of the Project: The host institute of the project is responsible for providing infrastructure support and hosting the project	https://www.iitkgp.ac.in
3	National Digital Library of India Office, Indian Institute of Technology Kharagpur	The administrative and infrastructural headquarters of the project	Dr. B. Sutradhar bsutra@ndl.gov.in
4	Project PI / Joint PI	Principal Investigator and Joint Principal Investigators of the project	Dr. B. Sutradhar bsutra@ndl.gov.in Prof. Saswat Chakrabarti will be added soon
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Characteristic genome rearrangements in experimental evolution of Saccharomyces cerevisiae.

Genome-wide regulatory complexity in yeast promoters: separation of functionally conserved and neutral sequence.

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Large-scale concatenation cDNA sequencing.

Calling Cards enable multiplexed identification of the genomic targets of DNA-binding proteins.

Oxford Nanopore sequencing, hybrid error correction, and de novo assembly of a eukaryotic genome

SCRaMbLE generates designed combinatorial stochastic diversity in synthetic chromosomes.

Detection of active transposable elements in Arabidopsis thaliana using Oxford Nanopore Sequencing technology

Structure of evolving populations of Saccharomyces cerevisiae: adaptive changes are frequently associated with sequence alterations involving mobile elements belonging to the Ty family.

Oxford Nanopore sequencing, hybrid error correction, and de novo assembly of a eukaryotic genome.

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