De novo genome sequence assembly of a filamentous fungus using Sanger, 454 and Illumina sequence data

doi:10.1186/gb-2009-10-9-r94

Genome Biology

Volume 10
Issue 9

Viewing options:

Abstract
Full text
PDF (1.3MB)
Additional files

Associated material:

PubMed record

Related literature:

Articles citing this article
on BioMed Central
on Google Scholar
on ISI Web of Science
on PubMed Central
Other articles by authors
on Google Scholar

DiGuistini S
Liao NY
Platt D
Robertson G
Seidel M
Chan SK
Docking TR
Birol I
Holt RA
Hirst M
Mardis E
Marra MA
Hamelin RC
Bohlmann J
Breuil C
Jones SJ

on PubMed

DiGuistini S
Liao NY
Platt D
Robertson G
Seidel M
Chan SK
Docking TR
Birol I
Holt RA
Hirst M
Mardis E
Marra MA
Hamelin RC
Bohlmann J
Breuil C
Jones SJ
Related articles/pages
on Google

on Google Scholar

on PubMed

Tools:

Post to:

Method

De novo genome sequence assembly of a filamentous fungus using Sanger, 454 and Illumina sequence data

Scott DiGuistini¹^* , Nancy Y Liao²^* , Darren Platt³ , Gordon Robertson² , Michael Seidel² , Simon K Chan² , T Roderick Docking² , Inanc Birol² , Robert A Holt² , Martin Hirst² , Elaine Mardis⁴ , Marco A Marra² , Richard C Hamelin⁵ , Jörg Bohlmann⁶ , Colette Breuil¹ and Steven JM Jones²

¹Department of Wood Science, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada

²BC Cancer Agency Genome Sciences Centre, Vancouver, BC, V5Z 4E6, Canada

³Amyris Biotechnologies, Inc., Hollis Street, Emeryville, CA 94608, USA

⁴Washington University School of Medicine, Forest Park Ave, St Louis, MO 63108, USA

⁵Natural Resources Canada, rue du PEPS, Ste-Foy, Quebec, G1V 4C7, Canada

⁶Michael Smith Laboratories, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada

author email corresponding author email* Contributed equally

Genome Biology 2009, 10:R94doi:10.1186/gb-2009-10-9-r94


Published:	11 September 2009

Subject areas: Bioinformatics, Genome studies, Methods

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.