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| 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 |
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