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Genome Biol. 2008;9(3):R55. doi: 10.1186/gb-2008-9-3-r55. Epub 2008 Mar 14.

Genome assembly forensics: finding the elusive mis-assembly.

Author information

1
Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD 20742, USA. amp@umiacs.umd.edu

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.

PMID:
18341692
PMCID:
PMC2397507
DOI:
10.1186/gb-2008-9-3-r55
[Indexed for MEDLINE]
Free PMC Article

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