Genotyping / sequencing tools and services

Inventory

Inventory is an open-source application that lets users collect inventory and weight data simultaneously. The app can perform as a standalone sample collection platform but is also compatible with Elane USB scales. These scales can be plugged directly into Android devices with USB OTG functionality. A USB hub can be used to allow both a scale and barcode scanner to run at the same time.

Highly Interactive Data Analysis Platform (HIDAP)

The Highly Interactive Data Analysis Platform (HIDAP) was developed for clonal crop breeders at the International Potato Center (CIP)

It is part of on-going efforts to unify best practices which practices include data collection, data quality and data analysis in clonal crop breeding. HIDAP builds on the former in-house tools DataCollector (DC) and CloneSelector (CS). These tools supported potato and sweetpotato breeding, respectively.

Sample Tracker

Sample Tracker is a web-based application developed by the International Maize and Wheat Improvement Center (CIMMYT) to facilitate the workflow and sample identity assignation and tracing around DNA sampling.

Sample tracker provides interfaces to load, generate and query scientist and project information, sample information, genotyping provider requisite plate layouts, plate layouts for lab implementation of DNA extraction, QC metric capture, DNA storage locations, sample file generation and shipping management.

SNPviewer

SNPviewer is a tool that enables genotyping data to be viewed as a cluster plot, but that does not include data analysis or reporting functionality.

Opening genotyping service project results in SNPviewer will allow you to view the genotyping clusters plate by plate. Genotyping calls cannot be changed within SNPviewer; if you need to be able to edit the calls then you will require our KlusterCaller software.

 

Coordinate

Coordinate replaces our previous DNA Plate App and Seed Tray App with a unified data collection app. Coordinate is based on defining templates and then collecting data in grids created from those templates. Two templates are included by default: Seed Tray and DNA Plate.

High-throughput genotyping services (HTPG)

High Throughput Genotyping Services (HTPG) is a shared KASPTM genotyping platform serving all CGIAR centers and their partner programs.

HTPG is established to provide low-cost and world class genotyping services to breeding programs working on the majority of CGIAR mandate crops. Current participating crops include Maize, Rice, Wheat, Groundnut, Chickpea, Pigeon Pea, Pearl Millet, Finger Millet, Sorghum, Potato, Common Bean, Cowpea, Cassava.

Biodiversity analysis with R (BIO-R)

Biodiversity analysis with R (BIO-R) is a set of R programs that do biodiversity analysis of molecular data, in order to calculate heterozygosity, diversity among and within groups, shannon index, number of effective allele, percent of polymorphic loci, Rogers distance, Nei distance, cluster analysis and multidimensional scaling 2D plot and 3D plot

You can include external groups for colored dendogram or MDS plots, and additionally obtain a Core Subset using molecular data and also phenotypic, geographical and any source of data.

Bayesian Generalized Linear Regression in R (BGLRR)

Bayesian Generalized Linear Regression in R (BGLRR) is a software to simplify the selection of input files and parameters to perform Bayesian Generalized Linear Regression using R (statistical software).

BGLR provides predictions, genome-wide association study (GWAS) analysis and analysis of reaction norm models. It allows the inclusion of markers information, relationship matrix (pedigree), environmental covariables, and other variables as fixed or random effects.

Spatial Multi-Environment Trial Analysis with R (Spatial META-R)

Spatial META-R is a software to simplify the selection of input files and parameters to perform spatial multi-environment trial analysis using R (statistical software) and ASReml v1.0 free version.

Spatial META-R provides the calculus of best linear unbiased estimates (BLUEs), best linear unbiased predictions (BLUPs), genetic correlations among locations and genetic correlations between variables, and broad-sense heritability. Analyses may be performed by location, across management conditions or across all locations.