CGIAR Polyploid Genomic Data Tools and Resources

CGIAR	Contact	Crop	Genotyping platforms used (eg GbS, Affymetrix Axiom, KASP etc)	Genotyping platform NEEDS/GAPS	Data formats used to store data (can copy and paste a small sample or attach a file in this page)	Data management tools used	Data management tools NEEDS /GAPS	Data analysis tools used	Data analysis tools NEEDS /GAPS	Requests for specific sessions not already covered in the agenda	Additional comments
CIP	Hannele Lindqvist-Kreuze	Potato	GbS, Intertek KASP, Illumina SNP array	affordable mid density genotyping system	fastq, vcf, excel	planning to use COPO	GOBII, sample tracking	GATK, bcftools, samtools, GWASpoly	GWAS with genotype probabilities and other data than biallelic SNP, estimating LD in polyploids
CIP	Dorcus Gemenet	Sweet potato	GBS, GBSpoly, IGSS, DArTseq	Low cost routine genotyping service, mid-density	FastQ, VCF, excel	Options available: sweetpotato base with GOBii backend, CIP		MAPpoly, QTLpoly, GATK, Picard tools, samtools, bcftools, BWA GWASpoly, GAPIT, AGHmatrix, TASSEL, GBSapp	Any method that can be applied to handle biallelic data with dosage or multi-allelic data with ease.
IITA	Trushar Shah	Banana	GbS, Intertek (KASP), Whole genome resequencing, DArTSeq, Illumina SNP chip, SSRs	Need an alternative for GbS or a provider at lower cost. Need to check if coverage (sequence depth) is enough for variant calling in polyploids?	FASTQ, VCF, Hapmap, DArT single row and two row format, Flapjack	Musabase, BTracT, R, Flapjack (Visualisation)	GOBII, DNA sample tracking (not specific to polyploids)	GATK, Fastx toolkit, Picard tools, Sam tools, VCFtools, BCFtools, PLINK	Tools to manipulate VCF files of polyploids. Filtering tools (vcf tools) don't work for polyploids Lindsay recommends an R package - VariantAnnotation (Bioconductor) Tools for mapping triploids.
Bioversity	Catherine Breton	Banana	SSR, GBS, RADseq, RNAseq		gVCF, VCF, FastQ, Fasta	GIGWA, Banana Genome Hub, Galaxy, Musabase		BWA, VCFTools, GATK, VCFHunter, TASSEL, R, Tablet, IGV, Picard tools, Samtools, BCFtools, PLINK	Tools for polyploids, vcf manipulating tools, mapping triploid Haplotypes reconstruction and inferences		Banana is also multiple ploidy levels (2x,3x,4x). cultivated ones are low fertile and vegetatively propagated. Triploids can be allopolyploid. it makes complex the use of GWAS difficult beyond diploids
IITA	Ranjana Bhattacharjee, Agre Paterne	Yam	GBS, DArTseq, WGRS	KASP, HTPG	VCF, HapMap, Raw format (DArTseq), FastQ	Linus, GATK, TASSEL, YamBase, R	Tools for polyploids, Galaxy, GOBII	VCFTools, R, PLINK, GATK, TASSEL, Flapjack, HISAT2, Tablet	Tools for polyploids; open source data management tools	It can be discussed in the beginning of the workshop.	Yam being multi-species with multiple ploidy levels, it would be good to know if the available tools can deal with multi-ploidy levels. Challenge - don’t know the ploidy level for Yam (single dose markers?)
CIAT	Luis Augusto	Forages
CIAT	Luis Augusto	Cassavava