Java applications for working with Illumina data and high-density molecular marker datasets
gbsTools is a program written in Java for demultiplexing paired-end Illumina data in a manner that retains sample-specific barcodes using fuzzy-matching.
OneMapTools uses VCF files containing multi-allelic molecular markers to generate the input files required by OneMap.
Python software for high-throughput digital image acquisition, pre-processing, and phenotyping of plant organs.
This software was originally designed to phenotype carrots, as described in this paper.
It makes uses of a standardized image layout to automate image acquisition, utilizing QR codes to handle file management, and features of known physical size to convert pixels to spatial resolution.
The OpenCV library is used to subsequently convert RGB images to binary masks, and measure various physical traits, which can be written to a MongoDB collection, or exported as CSV files. It is now primarily used for phenotyping hazelnuts: https://github.com/shbrainard/hazelnut-phenotyping.
This software was developed in collaboration with Julian Bustamante, a graduate student in the Spalding Lab at the University of Wisconsin-Madison, and Christoph Reimers, inventor of the skateboard trivet.