Skip to Content

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 <path to>/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/
                             http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0047768
                   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.
                '
Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are met: 
 
1. Redistributions of source code must retain the above copyright notice, this
   list of conditions and the following disclaimer. 
2. Redistributions in binary form must reproduce the above copyright notice,
   this list of conditions and the following disclaimer in the documentation
   and/or other materials provided with the distribution. 
 
        THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
        ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
        WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
        DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR
        ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
        (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
        LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
        ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
        (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
        SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 
The views and conclusions contained in the software and documentation are those
of the authors and should not be interpreted as representing official policies, 
either expressed or implied, of the FreeBSD Project.


about seo | product_software