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CGIARContactCropGenotyping platforms used (eg GbS, Affymetrix Axiom, KASP etc)Genotyping platform NEEDS/GAPSData formats used to store data (can copy and paste a small sample or attach a file in this page)Data management tools usedData management tools NEEDS /GAPSData analysis tools usedData analysis tools NEEDS /GAPSRequests for specific sessions not already covered in the agendaAdditional comments

CIP

Hannele Lindqvist-KreuzePotatoGbS, Intertek KASP, Illumina SNP arrayaffordable mid density genotyping systemfastq, vcf, excelplanning to use COPOGOBII, sample trackingGATK, bcftools, samtools, GWASpolyGWAS with genotype probabilities and other data than biallelic SNP, estimating LD in polyploids

CIP

Dorcus Gemenet 

Sweet potatoGBS, GBSpoly, IGSS, DArTseqLow cost routine genotyping service, mid-densityFastQ, VCF, excelOptions 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.

IITATrushar ShahBananaGbS, 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, FlapjackMusabase, 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. 



BioversityCatherine BretonBananaSSR, GBS, RADseq, RNAseq
gVCF, VCF, FastQ, FastaGIGWA, Banana Genome Hub, Galaxy, Musabase
BWA, VCFTools, GATK, VCFHunter, TASSEL, R, Linux, Tablet, IGV, Picard tools, Samtools, BCFtools, PLINK

Tools for polyploids, vcf manipulatemanipulating 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
IITARanjana Bhattacharjee, Agre PaterneYamGBS, DArTseq, WGRSKASP, HTPGVCF, HapMap, Raw format (DArTseq), FastQLinus, GATK, TASSEL, YamBase, RTools for polyploids, Galaxy, GOBIIVCFTools, R, PLINK, GATK, TASSEL, Flapjack, HISAT2, TabletTools for polyploids; open source data management toolsIt 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?)

CIATLuis AugustoForages








CIATLuis AugustoCassavava








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