Software
Genome assembly forensics: finding the elusive mis-assembly
Author affiliations
Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD 20742, USA
Citation and License
Genome Biology 2008, 9:R55 doi:10.1186/gb-2008-9-3-r55
Published: 14 March 2008Abstract
We present the first collection of tools aimed at automated genome assembly validation. This work formalizes several mechanisms for detecting mis-assemblies, and describes their implementation in our automated validation pipeline, called amosvalidate. We demonstrate the application of our pipeline in both bacterial and eukaryotic genome assemblies, and highlight several assembly errors in both draft and finished genomes. The software described is compatible with common assembly formats and is released, open-source, at http://amos.sourceforge.net webcite.
