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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*

  • * Corresponding author: Steven JM Jones sjones@bcgsc.ca

  • † Equal contributors

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

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

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

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

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

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

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Genome Biology 2009, 10:R94 doi:10.1186/gb-2009-10-9-r94

Published: 11 September 2009

Additional files

Additional data file 1:

Supplementary sections 1: additional explanation for the 454 read filtering and alignments of the 454 pre- and post- filtered Forge assemblies relative to the manually finished GCgb1 sequence. Supplementary sections 2: additional explanation and supporting figures for the filtering and trimming of Illumina PE read data. Supplementary sections 3: supporting Figure S5 detailing the read coverage in the final assembly as well as preliminary repeat annotations and highlighting a small number of misassemblies identified with Illumina PE alignment clusters.

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Open Data

Additional data file 2:

NCBI accession numbers for the trace data used in this study.

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Open Data