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. 




  • Bridges

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.

User Information

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Technical questions:

Send mail to remarks@psc.edu or call the PSC hotline: 412-268-6350.