@article{fdi:010053550,
  title = {{SN}i{P}lay : a web-based tool for detection, management and analysis of {SNP}s. {A}pplication to grapevine diversity projects},
  author = {{D}ereeper, {A}lexis and {N}icolas, {S}. and {L}e {C}unff, {L}. and {B}acilieri, {R}. and {D}oligez, {A}. and {P}eros, {J}. {P}. and {R}uiz, {M}. and {T}his, {P}.},
  editor = {},
  language = {{ENG}},
  abstract = {{B}ackground: {H}igh-throughput re-sequencing, new genotyping technologies and the availability of reference genomes allow the extensive characterization of {S}ingle {N}ucleotide {P}olymorphisms ({SNP}s) and insertion/deletion events (indels) in many plant species. {T}he 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. {R}esults: {I}n this context, we developed {SN}i{P}lay, a flexible, user-friendly and integrative web-based tool dedicated to polymorphism discovery and analysis. {I}t integrates: 1) a pipeline, freely accessible through the internet, combining existing softwares with new tools to detect {SNP}s and to compute different types of statistical indices and graphical layouts for {SNP} data. {F}rom standard sequence alignments, genotyping data or {S}anger sequencing traces given as input, {SN}i{P}lay detects {SNP}s and indels events and outputs submission files for the design of {I}llumina's {SNP} chips. {S}ubsequently, it sends sequences and genotyping data into a series of modules in charge of various processes: physical mapping to a reference genome, annotation (genomic position, intron/exon location, synonymous/non-synonymous substitutions), {SNP} frequency determination in user-defined groups, haplotype reconstruction and network, linkage disequilibrium evaluation, and diversity analysis ({P}i, {W}atterson's {T}heta, {T}ajima's {D}). {F}urthermore, the pipeline allows the use of external data (such as phenotype, geographic origin, taxa, stratification) to define groups and compare statistical indices. 2) a database storing polymorphisms, genotyping data and grapevine sequences released by public and private projects. {I}t allows the user to retrieve {SNP}s using various filters (such as genomic position, missing data, polymorphism type, allele frequency), to compare {SNP} patterns between populations, and to export genotyping data or sequences in various formats. {C}onclusions: {O}ur experiments on grapevine genetic projects showed that {SN}i{P}lay allows geneticists to rapidly obtain advanced results in several key research areas of plant genetic diversity. {B}oth the management and treatment of large amounts of {SNP} data are rendered considerably easier for end-users through automation and integration. {C}urrent developments are taking into account new advances in high-throughput technologies. {SN}i{P}lay is available at: http://sniplay.cirad.fr/.},
  keywords = {},
  booktitle = {},
  journal = {{B}mc {B}ioinformatics},
  volume = {12},
  numero = {},
  pages = {134},
  ISSN = {1471-2105},
  year = {2011},
  DOI = {10.1186/1471-2105-12-134},
  URL = {https://www.documentation.ird.fr/hor/fdi:010053550},
}