The folks in our Medical Genomics group have compiled a list of bioinformatics tools that are useful in the field of cancer genomics. The tools, mostly focused on next/second-generation sequence data, are organized by their purposes (sequence alignment, variant detection, annotation/pathway, significance analysis, group significance analysis, gene expression clustering, clinical correlation, cross-tumor analysis, and graphical/visualization). A lot of the tools were developed at The Genome Center, but they have also included tools from many different investigators that we find useful. Many, but unfortunately not all, of the tools are free/open source software.