SNiPlay : How to cite

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Pipeline for SNP analysis
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- General statistics
- VCFtools (stats)
- Polyploid analysis
- SNiPloid
- Chromosome Viewer
- Chromosome Viewer
- SNP density
- Diversity analysis
- EggLib
- VCFtools (sliding window)
- Population stratification
- sNMF
- Admixture
- IBD Kinship (Tassel)
- PCA / IBS matrix (plink)
- Distance tree (FastME)
- Association Studies
- GWAS Analysis
- Others
- Cytoscape
SNP Database
- Public datasets
- Download public datasets
- Queries
- SNP Queries V3
Documentation
- Manual pipeline V2
- Manual pipeline V3
How to cite
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How to cite

If you publish results obtained in part using SNiPlay, please cite required programs as follows:

Dereeper A, Homa F, Andres G, Sempere G, Sarah G, Hueber Y, Dufayard JF, Ruiz M. SNiPlay3: a web-based application for exploration and large scale analyses of genomic variations.. Nucleic Acids Res. 2015 Jul 1;43(W1) (PubMed)

External tools:

VCFtools: Danecek P, Auton A, Abecasis G, Albers CA, Banks E, DePristo MA, Handsaker RE, Lunter G, Marth GT, Sherry ST, McVean G, Durbin R; 1000 Genomes Project Analysis Group. The variant call format and VCFtools. Bioinformatics. 2011 Aug 1;27(15):2156-8. Epub 2007 Jul 25. (PubMed)
Admixture: D.H. Alexander, J. Novembre, and K. Lange. Fast model-based estimation of ancestry in unrelated individuals. Genome Research, 19:1655<96>1664, 2009. (PubMed)

A quasi-Newton method for accelerating the convergence of iterative optimization algorithms.

Phase: Stephens M., Scheet P. Accounting for decay of linkage disequilibrium in haplotype inference and missing-data imputation. Am J Hum Genet. 2005 Mar;76(3):449-62.(PubMed)
SeqLib library: De Mita S. http://seqlib.sourceforge.net. 2008. (SeqLib library)
Haplophyle: Sarah G., Ruiz M., Perrier X., Billot C. http://haplophyle.cirad.fr/index.jsp. 2007. (Haplophyle)
Gevalt: Davidovich O., Kimmel G., Shamir R. GEVALT: An integrated software tool for genotype analysis. BMC Bioinformatics. 2007 Feb 1;8:36. (PubMed)
Shape-IT: Delaneau O., Coulonges C, Zagury JF. Shape-IT: new rapid and accurate algorithm for haplotype inference. BMC Bioinformatics. 2008 Dec 16;9:540. (PubMed)
Blast: Altschul SF., Madden TL., Schaffer AA., Zhang J., Zhang Z., Miller W., Lipman DJ. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 1997 Sep 1;25(17):3389-402.(PubMed)
Polymorfind: Gaillard S. Foucher F., Pernet A. http://genhort.angers.inra.fr/projects/polymorfind/wiki/index.php/Polymorfind. 2008. (Polymorfind)