sniplay.southgreen.fr
SNiPlay : HomeSNiPlay is a web_based tool for SNP analysis: SNP detection, haplotype reconstruction, diversity analysis and linkage disequilibrium
http://sniplay.southgreen.fr/
SNiPlay is a web_based tool for SNP analysis: SNP detection, haplotype reconstruction, diversity analysis and linkage disequilibrium
http://sniplay.southgreen.fr/
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SNiPlay : Home | sniplay.southgreen.fr Reviews
https://sniplay.southgreen.fr
SNiPlay is a web_based tool for SNP analysis: SNP detection, haplotype reconstruction, diversity analysis and linkage disequilibrium
sniplay.southgreen.fr
SNiPlay : How to cite
http://sniplay.southgreen.fr/cgi-bin/citations.cgi
Pipeline for SNP analysis. Pipeline V2 (from Fasta). Pipeline V3 (from VCF). PCA / IBS matrix (plink). If you publish results obtained in part using SNiPlay, please cite required programs as follows:. 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. Genome Research, 19:1655. Altschu...
SNiPlay : Public data
http://sniplay.southgreen.fr/cgi-bin/public_data.cgi
Pipeline for SNP analysis. Pipeline V2 (from Fasta). Pipeline V3 (from VCF). PCA / IBS matrix (plink). Grapevine / Vitis vinifera. Nicolas et al, 2016. Genetic diversity, linkage disequilibrium and power of a large grapevine (Vitis vinifera L) diversity panel newly designed for association studies. SNPs (501 SNPs x 398 accessions) (Excel format). Bacilieri et al, 2016. Potential of combining morphometry and archeo-DNA information to investigate grapevine domestication. Cassava / Manihot esculenta.
SNiPlay : Datasets
http://sniplay.southgreen.fr/cgi-bin/datasets.cgi
Pipeline for SNP analysis. Pipeline V2 (from Fasta). Pipeline V3 (from VCF). PCA / IBS matrix (plink). Here are some example datasets that can be loaded to test the application:. Collection of FASTA alignments. Genotyping file (PED format).
SNP statistics along chromosomes (VCFtools)
http://sniplay.southgreen.fr/cgi-bin/vcftools.cgi
Pipeline for SNP analysis. Pipeline V2 (from Fasta). Pipeline V3 (from VCF). PCA / IBS matrix (plink). SNP statistics along chromosomes (VCFtools). 1 Load your data. Size of the sliding window (in bp):. 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.
SNiPlay : Documentation
http://sniplay.southgreen.fr/cgi-bin/documentation.cgi
Pipeline for SNP analysis. Pipeline V2 (from Fasta). Pipeline V3 (from VCF). PCA / IBS matrix (plink). SNiPlay combines two major components in a common Web interface: a set of pipelined programs and a relational database. The automated process consists of seven main modules and requires many additional in-house Perl modules to create junctions between the main programs (format compatibility) and to output the results in various formats (e.g. allelic files). 1) SNP / indel detection. Genotyping files mus...
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IRD Bioinformatics Homepage
http://bioinfo.mpl.ird.fr/index.php
You can register on cluster! Ask for portal account. Ask for cluster account. The IRD bioinformatics servers provides informatics and bioinformatics resources to four IRD research units (Plant and Health units) and their partners :. Is an information system developed to manage information on rice genetic resources collected or produced by IRD or CIRAD institutes. Is a comprehensive web resource for researchers working on Coffea genus, the Rubiaceae family or related species. INtracellular ParasitE CounTe...
IRD Bioinformatics
http://bioinfo.mpl.ird.fr/index.php/resources
You can register on cluster! Ask for portal account. Ask for cluster account. Is an information system developed to manage information on rice genetic resources collected or produced by IRD or CIRAD institutes. Is a comprehensive web resource for researchers working on Coffea genus, the Rubiaceae family or related species. Is a web-based tool that allows users to view comparisons of genetic and physical maps. more. The Xanthomonas utilities website. Is a web-based tool for SNP and polymorphism analysis.
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SNiPlay : Home
Pipeline for SNP analysis. IBS matrix / MDS plot (plink). New version: SNiPlay3 for managing large SNP datasets! It allows to manage SNPs derived from NGS technologies (WGRS, GBS, RNASeq.) and compute on the web series of tools for analyses at a whole-genome scale. SNiPlay offers two types of pipeline depending on input data format:. Pipeline V3: Analyze VCF files derived from SNP calling performed on NGS data (RNASeq, WGRS, GBS.). SNiPlay is part of the South Green bioinformatics platform.
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