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The coffee genome hub: a resource for coffee genomes

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Title The coffee genome hub: a resource for coffee genomes
 
Creator Dereeper, A.
Bocs, S.
Rouard, M.
Guignon, Valentin
Ravel, S.
Tranchant-Dubreuil, C.
Poncet, V.
Garsmeur, O.
Lashermes, P.
Droc, Gaëtan
 
Subject coffea
coffea canephora
data
data analysis
genomes
information systems
genetics
 
Description The whole genome sequence of Coffea canephora, the perennial diploid species known as Robusta, has been recently released. In the context of the C. canephora genome sequencing project and to support post-genomics efforts, we developed the Coffee Genome Hub (http://coffee-genome.org/), an integrative genome information system that allows centralized access to genomics and genetics data and analysis tools to facilitate translational and applied research in coffee. We provide the complete genome sequence of C. canephora along with gene structure, gene product information, metabolism, gene families, transcriptomics, syntenic blocks, genetic markers and genetic maps. The hub relies on generic software (e.g. GMOD tools) for easy querying, visualizing and downloading research data. It includes a Genome Browser enhanced by a Community Annotation System, enabling the improvement of automatic gene annotation through an annotation editor. In addition, the hub aims at developing interoperability among other existing South Green tools managing coffee data (phylogenomics resources, SNPs) and/or supporting data analyses with the Galaxy workflow manager.
 
Date 2015-01-28
2015-05-13T13:59:47Z
2015-05-13T13:59:47Z
 
Type Journal Article
 
Identifier Dereeper, A.; Bocs, S.; Rouard, M.; Guignon, V.; Ravel, S.; Tranchant-Dubreuil, C.; Poncet, V.; Garsmeur, O.; Lashermes, P.; Droc, G. (2015) The coffee genome hub: a resource for coffee genomes. Nucleic Acids Research 43 (D1): D1028-D1035. ISSN: 0305-1048
0305-1048
https://hdl.handle.net/10568/66031
https://doi.org/10.1093/nar/gku1108
https://dx.doi.org/10.7910/DVN/ZFQM2U
 
Rights CC-BY-4.0
Open Access
 
Format D1028-D1035
application/pdf
 
Publisher Oxford University Press (OUP)
 
Source Nucleic Acids Research 43 (D1)