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SNiPlay3: a web-based application for exploration and large scale analyses of genomic variations.

Dereeper A, Homa F, Andres G, Sempere G, Sarah G, Hueber Y, Dufayard JF, Ruiz M - Nucleic Acids Res. (2015)

Bottom Line: Version 3 now extends functionalities in order to easily manage and exploit SNPs derived from next generation sequencing technologies, such as GBS (genotyping by sequencing), WGRS (whole gre-sequencing) and RNA-Seq technologies.Based 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.Additionally, we developed a suite of Galaxy wrappers for each step of the SNiPlay3 process, so that the complete pipeline can also be deployed on a Galaxy instance using the Galaxy ToolShed procedure and then be computed as a Galaxy workflow.

View Article: PubMed Central - PubMed

Affiliation: UMR Interaction Plante-Microorganismes et Environnement (IPME), Institut de Recherche pour le Développement (IRD), BP 64501, 34394 Montpellier Cedex 5, France alexis.dereeper@ird.fr.

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Overview of the SNiPlay3 process. (A) General schema of the process and graphical layouts of the different modules. For modules marked with an asterisk, analyses are computed gene by gene. Input and output file formats are indicated in red. (B) One of the SNiPlay Galaxy workflows: the SNP calling workflow based on the GATK package for data pre-processing.
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Figure 1: Overview of the SNiPlay3 process. (A) General schema of the process and graphical layouts of the different modules. For modules marked with an asterisk, analyses are computed gene by gene. Input and output file formats are indicated in red. (B) One of the SNiPlay Galaxy workflows: the SNP calling workflow based on the GATK package for data pre-processing.

Mentions: An overview of the process is presented Figure 1A. The application offers numerous functionalities with attractive display layouts including GWAS, population structure, haplotype and linkage disequilibrium (LD) analyses, diversity analysis, SNP comparison between groups and general statistics about polymorphisms. Starting from a VCF file as entry point, the process first annotates the variants using an annotated reference genome to produce a new VCF file from which variants and genotyping data can be then mined and sent into a series of modules in charge of various processes. User has then the possibility to analyze variants either at the genome level or at the gene level. Most of the modules process genome-wide studies except for haplotype analyses—successively powered by the Gevalt software (8) for haplotype reconstruction and Haplophyle (9) for haplotype network—for which the analysis is done gene by gene or for user-defined genomic regions if do not exceed 200 variants (up to 200 regions). In this latter case, genes can be selected or directly provided as a list, while genomic regions can be defined by entering the limits, the application will loop and process these regions.


SNiPlay3: a web-based application for exploration and large scale analyses of genomic variations.

Dereeper A, Homa F, Andres G, Sempere G, Sarah G, Hueber Y, Dufayard JF, Ruiz M - Nucleic Acids Res. (2015)

Overview of the SNiPlay3 process. (A) General schema of the process and graphical layouts of the different modules. For modules marked with an asterisk, analyses are computed gene by gene. Input and output file formats are indicated in red. (B) One of the SNiPlay Galaxy workflows: the SNP calling workflow based on the GATK package for data pre-processing.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4489301&req=5

Figure 1: Overview of the SNiPlay3 process. (A) General schema of the process and graphical layouts of the different modules. For modules marked with an asterisk, analyses are computed gene by gene. Input and output file formats are indicated in red. (B) One of the SNiPlay Galaxy workflows: the SNP calling workflow based on the GATK package for data pre-processing.
Mentions: An overview of the process is presented Figure 1A. The application offers numerous functionalities with attractive display layouts including GWAS, population structure, haplotype and linkage disequilibrium (LD) analyses, diversity analysis, SNP comparison between groups and general statistics about polymorphisms. Starting from a VCF file as entry point, the process first annotates the variants using an annotated reference genome to produce a new VCF file from which variants and genotyping data can be then mined and sent into a series of modules in charge of various processes. User has then the possibility to analyze variants either at the genome level or at the gene level. Most of the modules process genome-wide studies except for haplotype analyses—successively powered by the Gevalt software (8) for haplotype reconstruction and Haplophyle (9) for haplotype network—for which the analysis is done gene by gene or for user-defined genomic regions if do not exceed 200 variants (up to 200 regions). In this latter case, genes can be selected or directly provided as a list, while genomic regions can be defined by entering the limits, the application will loop and process these regions.

Bottom Line: Version 3 now extends functionalities in order to easily manage and exploit SNPs derived from next generation sequencing technologies, such as GBS (genotyping by sequencing), WGRS (whole gre-sequencing) and RNA-Seq technologies.Based 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.Additionally, we developed a suite of Galaxy wrappers for each step of the SNiPlay3 process, so that the complete pipeline can also be deployed on a Galaxy instance using the Galaxy ToolShed procedure and then be computed as a Galaxy workflow.

View Article: PubMed Central - PubMed

Affiliation: UMR Interaction Plante-Microorganismes et Environnement (IPME), Institut de Recherche pour le Développement (IRD), BP 64501, 34394 Montpellier Cedex 5, France alexis.dereeper@ird.fr.

Show MeSH