Galaxy: Data intensive biology for everyone
Cloudman: Easily create compute clusters on the Cloud.
HiFive: Tools for handling HiC and 5C data
bx-python: Python package for working with genomic intervals, alignments, scores, etc.
ESPERR: Method for training classification models on multiple alignments and creating scores (e.g. Regulatory Potential).
MetaWRAP: Metagenomic data processing and genome extraction pipeline