This currently hosts two projects created and maintained by Adam English. Soon we'll be moving this page and only using sourceforge to host files and ticketing.
PBJelly - the genome upgrading tool.
PBHoney - the structural variation discovery tool
----- 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 -----
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
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