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Open Access Highly Accessed Correspondence

Limitations of the rhesus macaque draft genome assembly and annotation

Xiongfei Zhang, Joel Goodsell and Robert B Norgren,*

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Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE, 68198, USA

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Citation and License

BMC Genomics 2012, 13:206  doi:10.1186/1471-2164-13-206

Published: 30 May 2012

Abstract

Finished genome sequences and assemblies are available for only a few vertebrates. Thus, investigators studying many species must rely on draft genomes. Using the rhesus macaque as an example, we document the effects of sequencing errors, gaps in sequence and misassemblies on one automated gene model pipeline, Gnomon. The combination of draft genome with automated gene finding software can result in spurious sequences. We estimate that approximately 50% of the rhesus gene models are missing, incomplete or incorrect. The problems identified in this work likely apply to all draft vertebrate genomes annotated with any automated gene model pipeline and thus represent a pervasive challenge to the analysis of draft genomes.