Curation of Genome Assemblies by NCBI Tools and Resources

The increasing availability of genome sequences, together with genome analysis tools and resources, is advancing biological research. NCBI offers several resources that facilitate the analysis of assembly data, including the Assembly database, Genome pages, Clone DB and graphical displays, such as Map Viewer and Sequence Viewer. NCBI is also a member of the Genome Reference Consortium (GRC), which curates the human, mouse and zebrafish reference genome assemblies. As part of its involvement in this group, NCBI has developed a number of tools used to assess global and local assembly quality and manage curation activities. The use and application of these tools is not restricted to GRC-supported organisms and they have contributed to curation of other organisms’ reference assemblies, including chicken, chimpanzee and tomato. We will present results from our recent collaboration with members of Maize GDB utilizing GRC tools to assess the B73 v3 assembly. In addition, we will discuss our ongoing efforts to develop new resources for curation of whole genome shotgun (WGS) assemblies.

For organisms with complex genomic sequences, genomic clones remain an important resource in genome assembly and evaluation. The NCBI Clone DB, which facilitates association of these biological resources with genomic sequences, provides end-sequence based clone placements on the genome assemblies of more than 45 organisms. Graphical views of the placements are available on Clone DB webpages and the placement data is available for download from the Clone DB FTP site. We will demonstrate how to use Clone DB to find clones covering specific sequences and identify assembly regions associated with structural variation or possible assembly error.