SNiPlay: a web-based tool for detection, management and analysis of SNPs. Application to grapevine diversity projects

Background: High-throughput re-sequencing, new genotyping technologies and the availability of reference genomes allow the extensive characterization of Single Nucleotide Polymorphisms (SNPs) and insertion/deletion events (indels) in many plant species. The rapidly increasing amount of re-sequencing and genotyping data generated by large-scale genetic diversity projects requires the development of integrated bioinformatics tools able to efficiently manage, analyze, and combine these genetic data with genome structure and external data. Results: In this context, we developed SNiPlay, a flexible, user-friendly and integrative web-based tool dedicated to polymorphism discovery and analysis. It integrates: 1) a pipeline, freely accessible through the internet, combining existing softwares with new tools to detect SNPs and to compute different types of statistical indices and graphical layouts for SNP data. From standard sequence alignments, genotyping data or Sanger sequencing traces give...

• Type: Journal
• Year: 2011
• Where: BMCBI
• Authors: Alexis Dereeper, Stéphane Nicolas, Loic Le Cunff, Roberto Bacilieri, Agnes Doligez, Jean-Pierre Peros, Manuel Ruiz, Patrice This
• Keywords: Artificial Intelligence, BMCBI 2011, External Data, Genotyping, SNPs