PBJelly and PBHoney are not officially packaged within the same code. If you only want one of the tools, the presence of the second will not negatively affect anything you need.
Highlights of changes made to the PBSuite include:
- Improved functionality of PBHoney including 'force' calling, bug-fixes, better annotations and size estimations.
- PBJelly's output stage now has a parameter for the minimum number of reads required to support a gap fill before it's allowed to contribute to the improved assembly.
- New and improved tools for summarizing your data including BamStat.py, mapStat.py, quickN50.py, and summarizeAssembly.py.
As always, post questions and comments in the discussion page.
Have a great day,