AGORA: Assembly Guided by Optical Restriction Alignment
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
BMC Bioinformatics 2012, 13:189 doi:10.1186/1471-2105-13-189Published: 2 August 2012
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
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
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