Here are the changes you will find in the latest version of PBJelly
-- PBJelly's NCBISubmissionCreator now works and is much more user-friendly.
-- fillMetrics.json for any improved gap now has a [Left|Right|Span][Start|End] tag that keeps track of the coordinates of the contig that was used to left/right/span improve the gap.
-- Changed the untangling of reads in Support so it functions better.
-- Added exclusion.py for help with performing multiple iterations of PBJelly.py. exclusion.py will compare two support directories from PBJelly runs and remove reads that were previously identified as supporting a gap from being used in a successive iteration. Though, this is currently not optimal because there isn't a 1-to-1 correspondence between reads supporting the gaps and reads composing the contig that improves the gap (i.e. you lose some amount of data.)
In other news, the publicationon PBJelly has been submitted, revised, and resubmitted. Hopefully, it will be available on PLoS One soon. I'll keep you updated.