Genome assembly forensics finding the elusive mis-assembly.docVIP

Open Access So are 2008PhillippyetVoal.lumeftw9, Issue 3, Article R55 Genome assembly forensics: finding the elusive mis-assembly Adam M Phillippy, Michael C Schatz and Mihai Pop Address: Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD 20742, USA. Correspondence: Mihai Pop. Email: mpop@ Published: 14 March 2008 Received: 16 October 2007 Revised: 10 January 2008 Accepted: 14 March 2008 Genome Biology 2008, 9:R55 (doi:10.1186/gb-2008-9-3-r55) The electronic version of this article is the complete one and can be found online at /2008/9/3/R55 ? 2008 Phillippy et al.; licensee BioMed Central Ltd. This is an open access article distributed under the terms of the Creative Commons Attribution License (/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. DetectinganpdAfocrovlalelgenomeicdtaiotinnogfgmis-assemblysoftwareenome astoolssembisliecombineds./p for the first time in an automated pipeline for detecting large-scale genome assembly errors Abstract 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 . Rationale of quality. It has been difficult to gauge assembly quality by other means, because no automated validation tools exist. Sequence assembly errors exist in both draft and finished genomes. Since the initial draft sequence of the human genome was released in 2001 [1,2], great effort has been spent validating and