PBSuite Blog

After a long development cycle, The beta version of the new Jelly has arrived! Please download it, test it out, and send me your feedback. If you feel like waiting for the full release, you can expect a finalized program soon barring any major setbacks.

Below are the major changes in functionality. Soon we'll have a full report explaining what has changed and why. I'm not sure if this report will be an Applications Note in some journal or just a blog post.

Inter-Scaffold Gap Filling!
You asked for it, so I made it happen. Jelly now checks if a read maps concordantly off of two scaffold ends. If it does, that gap becomes a candidate for gap closing. Even if Jelly can't close the gap, the scaffold ends will be extended, thus giving your reference even more continuity.

Completely Re-factored Assembly Step!
We now use a more stringent assembly technique where we use the single best read supporting a gap as the backbone of the filling sequence. We then 'Polish' this sequence by mapping all other supporting reads onto it and performing a majority rules consensus calling. In our test datasets, this new technique closes fewer gaps - and thus has output references' continuity takes a hit - but there are far fewer mistakes in both base accuracy (an increase of about 3 percentage-points average accuracy) and in 'structure' accuracy (e.g. fewer gaps incorrectly forced closed).
Oh! And the new assembly step take only about 10seconds per-gap compared to 60secs in the old technique.

FastQ!
Jelly no longer requires a separate .fasta and .qual file. You can directly feed your fastq reads into Jelly. Don't have base qualities for your reference? No Problem! Jelly doesn't need that anymore. If you do have the reference quals, nothing has changed.

I want to Thanks all of the users who have been very engaging over the past year. I've really enjoyed helping you and learning what can be done to make better software - Not only from a functionality stand-point, but usability as well. I look forward to hearing about your experience with this new version.