Reference Genome Products
California Conservation Genomics Project on NCBI
Sequence data generated through the CCGP will comprise whole genome resequencing (WGS) from roughly 22,000 individuals from 150 genera and 230 unique species across the landscape of California. For most genera, to fully utilized the landscape WGS data, CCGP will additionally generate high quality reference genomes comprised of PacBio long read HiFi sequence data, Dovetail Omni-C conformational scaffolding data, and RNAseq based on Illumina short reads. In order to ensure that this truly massive data set is available not only to CCGP researchers, we will make all data publicly available through several genetic databases hosted by NCBI.
California Conservation Genomics Project assembly hub on UCSC Genome Browser
In addition to being accessioned on NCBI, the CCGP-generated reference genomes can also be found on the California Conservation Genomics Project assembly hub on the UC Santa Cruz Genome Browser. The UCSC Genome Browser serves as a comprehensive repository, allowing researchers and conservationists to explore and analyze genomic information associated with various species. It hosts a vast array of datasets, ranging from human genomes to model organisms and provides an intuitive interface for visualizing and analyzing genomic data. This tool enables users to delve into the genetic makeup of organisms, gaining insights into their evolutionary history, population dynamics, and adaptation strategies.
Metrics summary of CCGP genome assemblies
Contiguity metrics of CCGP genomes released on NCBI (only primary assembly/haplotype 1)
Functional completeness (BUSCO completeness) of CCGP genomes released on NCBI (only primary assembly/haplotype 1)
Species Genome Resources
