This currently hosts two projects created and maintained by Adam English.
PBJelly - the genome upgrading tool.
PBHoney - the structural variation discovery tool
Both are contained within the PBSuite code found in downloads.
----- PBJelly -----
Read The Paper
PBJelly is a highly automated pipeline that aligns long sequencing reads (such as PacBio RS reads or long 454 reads in fasta format) to high-confidence draft assembles. PBJelly fills or reduces as many captured gaps as possible to produce upgraded draft genomes.
----- PBHoney -----
Read The Paper
PBHoney is an implementation of two variant-identification approaches designed to exploit the high mappability of long reads (i.e., greater than 10,000 bp). PBHoney considers both intra-read discordance and soft-clipped tails of long reads to identify structural variants.
- Genome Assembly
- Genome Upgrade
- Structural Variation
- Assembly Evaluation
This is a nice tool, but very difficult to use. It could be improved greatly which could make it into really great software but there is nobody around to deal with real user issues... as seen by the lack of response in the online discussion forum. 1. If files are not in the expected format [eg. Fasta read names have to conform to an unadvertised standard], you do not get any warning or explanation why it failed. 2. If a stage fails, you do not get any notification. You have to search inside another file to find out whether it even worked. It should at least tell you "Errors happened. Look at <filename.err> for more details" or "No errors detected." 3. There is no easy way to take the best advantage of multiple cores. You can set an option within the Protocols XML file. And in some cases you can set an option via "-x" in the command line. But if I examine the load and CPU utilization of all cores, I can see that it rarely uses more than one core at the same time and in some stages, it never uses the number of cores specified. 4. Most of the user configurable options have unclear meaning. You have to read into the program code to figure out how they are really used. 5. Hardly any response to user input. There is a discussion forum but virtually no activity or response from anyone involved with the software. It appears to be abandon-ware.
Easy to use and fast. Did a great job of filling in stretches of N's in my scaffold with low coverage PacBio data.
Pb-jelly is excellent! Thanks.
pb-jelly is small and works nicely