Jelly

About the Software

Logo for PBSuitePBJelly 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 Paper

BMC Bioinformatics: PBHoney: Identifying Genomic Variants via Long-Read Discordance and Interrupted Mapping

System Requirements

  • Blasr (https://github.com/PacificBiosciences/blasr) Version 1.3.1.127046 is fully vetted as compatible with Jelly. Other versions may run into problems. Use  > blasr -version to figure out what you have. Blasr must be in your environment path.
  • Python 2.7
    • Python must be in your environment path and executable with the commands:
      • > python
      • > /usr/bin/env python
  • Networkx v1.1
    • Versions past v1.1 have been shown to have many issues. This will be updated in the future. To check your version use, in a python interactive terminal, type:
      • > import networkx
      • > networkx.__version__
    • If you get an error saying the attribute isn't found, you don't have version 1.1

Installation

  1. Edit setup.sh and change $SWEETPATH to the full directory where you've placed the package.
  2. To automatically place the package into your environment, add > source /setup.sh to your .bash_profile.
  3. Be sure to source your .bash_profile (or just setup.sh) before using Jelly.

Download

https://sourceforge.net/projects/pb-jelly/

README

Jelly README

License

Copyright © Baylor College of Medicine Human Genome Sequencing Center. All rights reserved.

               Contributors: Adam English (english@bcm.edu)
                Affiliation: Human Genome Sequencing Center
                        URL: http://www.hgsc.bcm.tmc.edu/
                             https://sourceforge.net/projects/pb-jelly/
                   Citation: English, Adam C., Stephen Richards, Yi Han, Min Wang,
                             Vanesa Vee, Jiaxin Qu, Xiang Qin, et al. “Mind the
                             Gap: Upgrading Genomes with Pacific Biosciences RS
                             Long-Read Sequencing Technology.” PLoS ONE 7, no. 11
                             (November 21, 2012): e47768.
                             doi:10.1371/journal.pone.0047768.
                '
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