Genome assembly forensics: finding the elusive mis-assembly
Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD 20742, USA
Genome Biology 2008, 9:R55 doi:10.1186/gb-2008-9-3-r55Published: 14 March 2008
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.