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.
- PBJelly web site
- PBJelly Sourceforge page
- BMC Bioinformatics: PBHoney: Identifying Genomic Variants via Long-Read Discordance and Interrupted Mapping
- English AC, Richards S, Han Y, Wang M, Vee V, Qu J, et al. (2012) Mind the Gap: Upgrading Genomes with Pacific Biosciences RS Long-Read Sequencing Technology. PLoS ONE 7(11): e47768.
To see what versions of PBJelly are available type
module avail pbjelly
To see what other modules are needed, what commands are available and how to get additional help type
module help pbjelly
To use PBJelly, include a command like this in your batch script to load the PBJelly module:
module load pbjelly
Be sure you also load any other modules needed, as listed by the
module help pbjelly command.