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Evaluate Genome Annotation Quality

The first human genome was sequenced at a cost of $2.7 billion. Today, only in 20 years, a “high-quality” genome can be generated for about $1000. As the innovation in genome-sequencing technologies and strategies does not appear to slow down, we expect continue booms in the number of sequenced and annotated genomes. Generating a high-quality genome annotations is a complex and challenging problem. As genome annotation is an iterative process, tools to track quality of annotated genomes from release-to-release and iteration-to-iteration are badly required. In this tutorial, we are using GenomeQC to generate a comprehensive summary of genome annotation statistics and benchmark against gold standard reference annotations (Manchanda et al., 2019). GenomeQC can be used both as an app in the DE and as a downstream analysis tool for WQ-MAKER on JetStream.

References

GenomeQC: A quality assessment tool for genome assemblies and gene structure annotations. Nancy Manchanda, John L. Portwood II, Margaret R. Woodhouse, Arun S. Seetharam, Carolyn J. Lawrence-Dill, Carson M. Andorf, Matthew B. Hufford. bioRxiv, posted October 8, 2019 (doi: 10.1101/795237)

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