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Open Access Highly Accessed Research article

Assessing pooled BAC and whole genome shotgun strategies for assembly of complex genomes

Niina Haiminen1*, F Alex Feltus23 and Laxmi Parida1

Author Affiliations

1 IBM T.J. Watson Research Center, P.O. Box 218, Yorktown Heights, NY 10598, USA

2 Department of Genetics & Biochemistry, Clemson University, Clemson, SC 29634, USA

3 Clemson University Genomics Institute, Clemson University, Clemson, SC 29634, USA

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BMC Genomics 2011, 12:194  doi:10.1186/1471-2164-12-194

Published: 15 April 2011

Additional files

Additional file 1:

Read coverage combinations. Table of possible read coverage combinations.

Format: DOC Size: 62KB Download file

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Additional file 2:

Default vs. optimized assembly parameters. Figure comparing default and optimized assembly parameters for 3Mbp assemblies of five genomes.

Format: PPT Size: 742KB Download file

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Additional file 3:

Arabidopsis pooled BAC assembly statistics. Table with Arabidopsis pooled BAC assembly statistics.

Format: XLS Size: 39KB Download file

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Additional file 4:

Detailed Arabidopsis pooled BAC assembly statistics. Table showing detailed Arabidopsis assembly statistics for 3Mbp and 12Mbp pool assemblies.

Format: XLS Size: 263KB Download file

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Additional file 5:

Arabidopsis pools' assembly scores. Table showing assembly evaluation scores for Arabidopsis pool assemblies.

Format: XLS Size: 57KB Download file

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Additional file 6:

Reference sequences. Table showing reference sequences and coordinates for studied source genomes.

Format: DOC Size: 32KB Download file

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Additional file 7:

CABOG assembly statistics. Tar archive containing CABOG assembly statistics for each assembly in our simulation study.

Format: ZIP Size: 944KB Download file

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Additional file 8:

Arabidopsis genome pools' assembly scores. Table showing assembly scores for individual pseudomolecules of each 3Mbp pool for the Arabidopsis genome.

Format: DOC Size: 97KB Download file

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Additional file 9:

Arabidopsis genome pools' repeat content vs. assembly scores. Figure showing repeat content and scores for Arabidopsis whole genome pool assemblies.

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