My lab develops software tools for use in developing and distributing our methods. Our goals including releasing all of our software under a liberal open-source license such as the Apache License, v2.0, easy to use, and accompanied by documentation.
Asaph is a software package for analyzing SNP data. Asaph primarily supports association testing (including our methods for handling missing data) and inversion detection using PCA and association testing.
PeakMatcher is a simple tool we developed to match peaks from DNA enrichment assays across genome assemblies. As genome assemblies are improved through new sequencing methods, DNA enrichment assay data need to be re-analyzed using the new assemblies. PeakMatcher provides scripts for comparing called peaks on the same genome (e.g., to validate pipeline parameters or compare agreement across different assays) or different genomes using the raw reads (e.g., to validate that peaks are not lost with the new genome assembly or identify new peaks for analysis).