conference schedule and program with abstracts - Horticulture ...
conference schedule and program with abstracts - Horticulture ...
conference schedule and program with abstracts - Horticulture ...
You also want an ePaper? Increase the reach of your titles
YUMPU automatically turns print PDFs into web optimized ePapers that Google loves.
P-37<br />
A. Dereeper <strong>and</strong> P. This*<br />
SNiPlay, a web application for SNP analysis<br />
DIAPC INRA-Montpellier Supagro, Montpellier, France<br />
*Corresponding author: this@supagro.inra.fr<br />
Sequencing <strong>and</strong> large scale genetic diversity projects have simultaneously increased in<br />
grapevine. As a consequence, the need to automatically detect polymorphisms <strong>and</strong> exploit<br />
subsequent sequence <strong>and</strong> genotyping data are growing accordingly. Here, we present SNiPlay, a<br />
web-based tool dedicated to SNP discovery <strong>and</strong> polymorphism analysis. It integrates a pipeline,<br />
freely accessible through the internet, combining existing software to compute different kinds of<br />
analysis. From allelic data, alignment, or sequencing traces given as input (notably using the<br />
Polymorfind <strong>program</strong>), it detects SNP <strong>and</strong> insertion/deletion events. Then it sends sequences <strong>and</strong><br />
allelic data into an integrative pipeline able to achieve successive steps:<br />
- Mapping on the Vitis vinifera (‘Pinot’) reference genome <strong>and</strong> SNP annotation (genomic<br />
position, intron/exon, synonyme/non synonyme)<br />
- Haplotype reconstruction (using softwares Phase, Gevalt or ShapeIT)<br />
- Haplotype network (Haplophyle)<br />
- Linkage Disequilibrium (Haploview)<br />
- Diversity analysis (SeqLib library)<br />
It also includes a database to store polymorphism <strong>and</strong> genotyping data produced by projects on<br />
grapevine, notably SNPGrapeMap <strong>and</strong> DLVitis projects. Private access allows collaborators to<br />
explore data: SNP retrieval using various filters (genomic position, missing data, polymorphism<br />
type), comparison of SNPs between populations or other external information about accessions<br />
(geographical origin <strong>and</strong> phenotypic data), <strong>and</strong> export of genotype data in different formats. This<br />
database can collect <strong>and</strong> combine genotyping data coming from sequencing project as well as<br />
those obtained by Illumina chips <strong>and</strong> provides a section facilitating comparison between<br />
experiments. Finally, we plan to add a specific module able to manage <strong>and</strong> detect SNP from<br />
Next-Generation Sequencing data soon. Furthermore, SNiPlay is flexible enough to easily<br />
incorporate in the future new modules able to manage other kinds of analyses such as kinship,<br />
association studies, or population structure.<br />
SNiPlay is available at http://sniplay.cirad.fr.<br />
113