An integrated, scalable, high-performance-computing pipeline that combines genome comparison tools, probe design software. TOFI incorporates major algorithmic improvements, resulting in performance that is nearly up to five-times faster than the previous version of the pipeline. The use of multiple specificity criteria provides finer control over the number of resulting fingerprints. This tool could also be used as a sequence alignment programs in order to design highly specific microarray probes for a given target pathogen.
A package that provides an extension of the RangedSummarizedExperiment class with additional API features. This class provides convenient and fast methods for working with segmented genomic data. Additionally, GenoSet provides the class RleDataFrame which stores runs of data along the genome for multiple samples and provides very fast summaries of arbitrary row sets (regions of the genome).