@article{fdi:010064929,
  title = {{SN}i{P}lay3 : a web-based application for exploration and large scale analyses of genomic variations},
  author = {{D}ereeper, {A}lexis and {H}oma, {F}. and {A}ndres, {G}. and {S}empere, {G}. and {S}arah, {G}. and {H}ueber, {Y}ann and {D}ufayard, {J}. {F}. and {R}uiz, {M}.},
  editor = {},
  language = {{ENG}},
  abstract = {{SN}i{P}lay is a web-based tool for detection, management and analysis of genetic variants including both single nucleotide polymorphisms ({SNP}s) and {I}n{D}els. {V}ersion 3 now extends functionalities in order to easily manage and exploit {SNP}s derived from next generation sequencing technologies, such as {GBS} (genotyping by sequencing), {WGRS} (whole gresequencing) and {RNA}-{S}eq technologies. {B}ased on the standard {VCF} (variant call format) format, the application offers an intuitive interface for filtering and comparing polymorphisms using user-defined sets of individuals and then establishing a reliable genotyping data matrix for further analyses. {N}amely, in addition to the various scaled-up analyses allowed by the application (genomic annotation of {SNP}, diversity analysis, haplotype reconstruction and network, linkage disequilibrium), {SN}i{P}lay3 proposes new modules for {GWAS} (genome-wide association studies), population stratification, distance tree analysis and visualization of {SNP} density. {A}dditionally, we developed a suite of {G}alaxy wrappers for each step of the {SN}i{P}lay3 process, so that the complete pipeline can also be deployed on a {G}alaxy instance using the {G}alaxy {T}ool{S}hed procedure and then be computed as a {G}alaxy workflow. {SN}i{P}lay is accessible at http://sniplay.southgreen.fr.},
  keywords = {},
  booktitle = {},
  journal = {{N}ucleic {A}cids {R}esearch},
  volume = {43},
  numero = {{W}1},
  pages = {{W}295--{W}300},
  ISSN = {0305-1048},
  year = {2015},
  DOI = {10.1093/nar/gkv351},
  URL = {https://www.documentation.ird.fr/hor/fdi:010064929},
}