Welcome to PBSuite!

If you check in Files tab, you'll see two new downloads - PBSuite and PBHoney. I apologize that it's poorly organized and will be cleaning it up soon.

The reason for these new files is I've been building a new program called PBHoney. Because there are so many useful utilities in PBJell's code-base, I decided to build PBHoney as an extension of PBJelly. This has given birth to what this project will be called from here on out - the PBSuite (suite.. sweet.. get it!?).

If you want just PBJelly, or just PBHoney, I'll make those tools available separately for a while longer. If you want the entire package, download what may eventually become the only release, the PBSuite.

Now, while PBHoney has been built primarily to function as a structural variation (SV) caller, it's also applicable as a mis-assembly discovery tool. Abstractly, an SV is simply a difference in the sample genome when compared to a reference. Therefore, if you de-novo assemble a set of reads and then attempt to discover SVs in your new assembly using your original set of input reads, anything discovered is either the result of a non-homozygous allele in your sample or a mis-assembly.

There will be much more work with details and results coming out for this soon. Our paper is in submission and once we build a proper website we'll post slides, notes, lectures, and visually attractive versions of the README.txt files. The HoneyReadme.txt has lots of details about how to find SVs with PBHoney and one day we'll have equally awesome documents highlighting PBHoney's mis-assembly capabilities.

--
Have a great day,
~/Adam English