Software

Genome assembly forensics: finding the elusive mis-assembly

Adam M Phillippy , Michael C Schatz and Mihai Pop

Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD 20742, USA

author email corresponding author email

Genome Biology 2008, 9:R55doi:10.1186/gb-2008-9-3-r55

Published:	14 March 2008

Subject areas: Bioinformatics, Genome studies

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 http://amos.sourceforge.net webcite.