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De novo genome sequence assembly of a filamentous fungus using Sanger, 454 and Illumina sequence data DiGuistini, Scott; Liao, Nancy Y.; Platt, Darren; Robertson, Gordon; Seidel, Michael; Chan, Simon K.; Docking, T. R.; Birol, Inanc; Holt, Robert A.; Hirst, Martin; Mardis, Elaine; Marra, Marco, 1966-; Hamelin, Richard C.; Bohlmann, Jörg; Breuil, Colette; Jones, Steven J. M.

Abstract

Sequencing-by-synthesis technologies can reduce the cost of generating de novo genome assemblies. We report a method for assembling draft genome sequences of eukaryotic organisms that integrates sequence information from different sources, and demonstrate its effectiveness by assembling an approximately 32.5 Mb draft genome sequence for the forest pathogen Grosmannia clavigera, an ascomycete fungus. We also developed a method for assessing draft assemblies using Illumina paired end read data and demonstrate how we are using it to guide future sequence finishing. Our results demonstrate that eukaryotic genome sequences can be accurately assembled by combining Illumina, 454 and Sanger sequence data.

Item Metadata

Title
De novo genome sequence assembly of a filamentous fungus using Sanger, 454 and Illumina sequence data
Creator
DiGuistini, Scott; Liao, Nancy Y.; Platt, Darren; Robertson, Gordon; Seidel, Michael; Chan, Simon K.; Docking, T. R.; Birol, Inanc; Holt, Robert A.; Hirst, Martin; Mardis, Elaine; Marra, Marco, 1966-; Hamelin, Richard C.; Bohlmann, Jörg; Breuil, Colette; Jones, Steven J. M.
Contributor
Michael Smith Laboratories
Publisher
BioMed Central
Date Issued
2009-09-11
Description
Sequencing-by-synthesis technologies can reduce the cost of generating de novo genome assemblies. We report a method for assembling draft genome sequences of eukaryotic organisms that integrates sequence information from different sources, and demonstrate its effectiveness by assembling an approximately 32.5 Mb draft genome sequence for the forest pathogen Grosmannia clavigera, an ascomycete fungus. We also developed a method for assessing draft assemblies using Illumina paired end read data and demonstrate how we are using it to guide future sequence finishing. Our results demonstrate that eukaryotic genome sequences can be accurately assembled by combining Illumina, 454 and Sanger sequence data.
Genre
Article
Type
Text
Language
eng
Date Available
2015-11-05
Provider
Vancouver : University of British Columbia Library
Rights
Attribution 4.0 International (CC BY 4.0)
DOI
10.14288/1.0167807
URI
http://hdl.handle.net/2429/55168
Affiliation
Forestry, Faculty of; Wood Science, Department of; Non UBC
Citation
Genome Biology. 2009 Sep 11;10(9):R94
Publisher DOI
10.1186/gb-2009-10-9-r94
Peer Review Status
Reviewed
Scholarly Level
Faculty
Copyright Holder
DiGuistini et al..
Rights URI
http://creativecommons.org/licenses/by/4.0/
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Attribution 4.0 International (CC BY 4.0)