Open Access Highly Accessed Methodology article

AGORA: Assembly Guided by Optical Restriction Alignment

Henry C Lin1, Steve Goldstein234, Lee Mendelowitz15, Shiguo Zhou234, Joshua Wetzel6, David C Schwartz234 and Mihai Pop1*

Author Affiliations

1 Center for Bioinformatics and Computational Biology, University of Maryland-College Park, College Park, MD, USA

2 Laboratory for Molecular and Computational Genomics, University of Wisconsin-Madison, Madison, WI, USA

3 Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI, USA

4 Department of Chemistry, University of Wisconsin-Madison, Madison, WI, USA

5 Applied Mathematics and Scientific Computation Program, University of Maryland-College Park, College Park, MD, USA

6 Department of Computer Science, and Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA

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BMC Bioinformatics 2012, 13:189  doi:10.1186/1471-2105-13-189

Published: 2 August 2012

Additional files

Additional file 1:

Per-genome results of assembling each genome. An excel spreadsheet detailing the results of assembling 369 bacterial genomes with AGORA, given optical maps simulated with three different error rates.

Format: XLS Size: 287KB Download file

This file can be viewed with: Microsoft Excel Viewer

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Additional file 2:

Figure showing the impact of starting N50 size of the de Bruijn graph on sequence correctness. A plot showing the sequence correctness of 369 bacterial genome assemblies by AGORA versus the starting N50 size of their de Bruijn graphs, under three different optical map error rates. Genomes with starting N50 size greater than 50 kbp are generally assembled with higher than 98% correctness over all three error rates, while the results are mixed for genomes with lower starting N50 size.

Format: PNG Size: 40KB Download file

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Additional file 3:

AGORA source code. A zip file containing the code used to generate the results presented in our paper.

Format: ZIP Size: 41KB Download file

Open Data