ARCAD BioInformatics Portal

The ARCAD BioInformatics Portal provides access to data produced by the ArCad project.

New reference transcriptomes

We produced a unique large dataset of reference transcriptomes to provide new knowledge about the evolution of plant genomes and crop domestication. We validated an assembly protocol of RNA-Seq data for comparative population genomics and we used the same protocol for the release of 29 new transcriptomes of crop plants and wild relatives. The species list has a large taxonomic representation with the inclusion of 15 monocots and 14 eudicots. All the contigs were annotated using Blast, Prot4EST, and Blast2GO. To get data : click to Organisms, select your species, then click to Downloads. For coffee and coffee out-groups access is still private. Authors who use and download data from the ARCAD BioInformatics Portal are encouraged to cite Sarah, G. et al., A large set of 26 new reference transcriptomes dedicated to comparative population genomics in crops and wild relatives, 2014.

Transcriptome population genomics in African rice

Here, data associated with the study Nabholz et al. 2014, Transcriptome population genomics reveals severe bottleneck and domestication cost in the African rice (O. glaberrima), Mol Ecol. 2014 Mar 30. Here, corresponding sources codes, executables, scripts and detailed informations for the ABC (Approximate Bayesian Analysis) analysis and population genetic statistics.

Scripts for the analysis of high-throughput sequencing data

We developed a package gathering scripts for the analysis of high-throughput sequencing data from the ARCAD project. This package is available at https://github.com/SouthGreenPlatform/arcad-hts.
 

The ARCAD BioInformatics Portal is a component of the South Green Bioinformatics Platform (http://southgreen.cirad.fr/).