Updated NGS data processing toolkit. Programs for working with FASTQ, FASTA, BAM, VCF, BED, GTF, and tab-delimited text annotation files. (active development)
Splicing analysis toolkit. Used for finding novel splice junctions and differential splicing analysis.
Smith-Waterman local alignment library/tool
Language for defining and running pipelines on HPC clusters
Single user batch job scheduler for workstations
Program for viewing and working with tab-delimited text files (and CSV).
Find peaks in kernel density estimate (KDE) matrices
Common utility classes useful for Java projects
Framework for developing Java command-line applications that have a *nix feel
Original NGS data processing toolkit (maintenance only)
Utility progams for working with tab-delimited text files
Download files / samples from Illumina's BaseSpace