Genome assembly forensics: finding the elusive mis-assembly

We present the first collection of tools aimed at automated genome assembly validation. This paper formalizes several mechanisms for detecting mis-assemblies, and describes their implementation in our automated validation pipeline, 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.