The deepTools developers have released a brand new version! This time with CRAM support, new normalization and plotting options, new tools, e.g. alignmentsieve for ATAC-seq, and many more.

deepTools 3.0 is now available on pypi (bioconda soon). Changes include a completely revamped normalization interface (and new methods), CRAM support, interactive plots, a more homogenized interface, new tools and better MultiQC integration

— Devon Ryan (@dpryan79) 12. Februar 2018

Special thanks to Devon and Fidel for those fantastic tools that were executed over 50.000 times so far on our Galaxy server.