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The Candida Genome Database (CGD): incorporation of Assembly 22, systematic identifiers and visualization of high throughput sequencing data

The Candida Genome Database (CGD, http://www.candidagenome.org/) is a freely available online resource that provides gene, protein and sequence information for multiple Candida species, along with web-based tools for accessing, analyzing and exploring these data. The mission of CGD is to facilitate and accelerate research into Candida pathogenesis and biology, by curating the scientific literature in real time, and connecting literature-derived annotations to the latest version of the genomic sequence and its annotations. Here, we report the incorporation into CGD of Assembly 22, the first chromosome-level, phased diploid assembly of the C. albicans genome, coupled with improvements that we have made to the assembly using additional available sequence data. We also report the creation of systematic identifiers for C. albicans genes and sequence features using a system similar to that adopted by the yeast community over two decades ago. Finally, we describe the incorporation of JBrowse into CGD, which allows online browsing of mapped high throughput sequencing data, and its implementation for several RNA-Seq data sets, as well as the whole genome sequencing data that was used in the construction of Assembly 22.

Authors:   Socheata Ly; Deanna M. Navaroli; Marie-Cécile Didiot; James Cardia; Lakshmipathi Pandarinathan; Julia F. Alterman; Kevin Fogarty; Clive Standley; Lawrence M. Lifshitz; Karl D. Bellve; Matthieu Prot; Dimas Echeverria; Silvia Corvera; Anastasia Khvorova
Journal:   Nucleic Acids Research
Volume:   45
edition:   1
Year:   2017
Pages:   15
DOI:   10.1093/nar/gkw1005
Publication date:   09-Jan-2017
Facts, background information, dossiers
  • whole genome sequencing
  • RNA
  • Research
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