This repository concern the SNiPlay part of the GFLS project (website). It is made in collaboration with Alexis Dereeper from the 'Institut de Recherche pour le Développement' (IRD). All the XML files (Wrappers) are made by his team.
The repository contain all the wrappers for the workflow SNiPlay.
- admixture [deprecated]
- fastme
- plink
- readseq
- snmf
- snpeff_from_gff_vcf
- tassel5
- vcftools_filter_stats_diversity (vcftoolsFilter,vcftoolsStats,vcftoolsSlidingWindow)
- mlmm
Wrappers for the Haplotype analysis workflow.
- Beagle
- Haplophyle
It contain also wrappers for SNP analysis (in Sniplay repo.).
- AnnotationStatsFromVCF
- check_gwas_inputs
- egglib
- GetHaplotypesFromPhasedVCF
- hapmap2mlmm
- MDSplot
- ped2bed
- PedToFasta
- Rooting
- SNP_density
- VCF2Hapmap
The sniplay3_complete_workflow repository.
And the Haplotype_analysis workflow repository.
Alexis Dereeper, Felix Homa, Gwendoline Andres, Guilhem Sempere, Gautier Sarah, Yann Hueber, Jean-François Dufayard, Manuel Ruiz; SNiPlay3: a web-based application for exploration and large scale analyses of genomic variations, Nucleic Acids Research, Volume 43, Issue W1, 1 July 2015, Pages W295–W300, https://doi.org/10.1093/nar/gkv351
Alexis Dereeper, Stéphane Nicolas, Loïc Le Cunff, Roberto Bacilieri, Agnès Doligez, Jean-Pierre Peros, Manuel Ruiz and Patrice This; SNiPlay: a web-based tool for detection, management and analysis of SNPs. Application to grapevine diversity projects, BMC Bioinformatics, Volume 12, 5 May 2011, Page 134, https://doi.org/10.1186/1471-2105-12-134
These tools are available in a docker container: