Quercus lobata - Reference Genome

Summary
Details
Publications
Description and Download
Summary
Publication
Sork, V. L., Fitz-Gibbon, S. T., Puiu, D., Crepeau, M., Gugger, P. F., Sherman, R., ... & Salzberg, S. L. (2016). First draft assembly and annotation of the genome of a California endemic oak Quercus lobata Née (Fagaceae). G3: Genes, Genomes, Genetics, g3-116. http://www.g3journal.org/content/6/11/3485
Name
Quercus lobata - Reference Genome
Resource Type
Genome Assembly
Organism
Q. lobata (Valley Oak)
Details
Program, Pipeline, Workflow or Method Name
Cufflinks
Program Version
cufflinks-2.2.1.Linux_x86_64/gffread
Date Performed
Thursday, April 6, 2017 - 21:00
Data Source
Source Name
: Qlobata_Genome1.0.fasta
Cross Reference
NCBI BioProject:308314
Description and Download

Quercus lobata Genome
Version 3.0, 1.0 and 0.5

Sork VL, Fitz-Gibbon ST, Puiu D, Crepeau M, Gugger PF, Sherman R, Stevens K, Langley CH, Pellegrini M, Salzberg SL. Quercus lobata Née (Fagaceae). G3: Genes|Genomes|Genetics. 2016 Nov 1;6(11):3485-95.

More information can be found at the Valley Oak Genome Project.

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The Valley Oak genome has two assemblies available. We are hosting genes and genomic scaffolds from version 1.0, which has not been haplotyped reduced and up to one third of the genome may be present in two copies. A haplotype reduced version, 0.5, is also available from the Valley Oak Genome Project and as downloads below. In 0.5, most genomic regions are represented once but up to 100Mb is missing. More information can be found in the publication and the Valley Oak Genome Project page.

Downloads

Version 0.5

Valley Oak Genome 0.5 (reduced) sequences
Valley Oak Genome 0.5 (reduced) annotation
SNPs and SMVs

Version 1.0

Valley Oak Genome 1.0 sequences
Valley Oak Genome 1.0 annotation

Version 3.0

Coding Sequence 3.0 (fasta format)
Protein Sequences 3.0 (fasta format)
Genome 3.0 annotation
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