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Honey

About the Software

Logo for PBSuitePBHoney 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.

System Requirements

  • samtools 0.1.17
  • blasr 1.3.1.127046        
  • python 2.7
  • h5py 2.0.1
  • pysam 0.7.4         
  • numpy 1.6

Note: If you have PacBio's SMRTAnalysis suite v2.1, all of these requirements will be met.

Installation

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

Quick Start

For more details on each step in the pipeline, see the README below.
 
Beginning with a mapped bam, you'll use Honey.py to execute the stages 'pie', 'tails', 'spots'.

  1. Honey.py pie
    1. Extract the soft-clipped tails and attempt to remap them
  2. Honey.py tails
    1. Cluster the tail-mapping information to make genomic breakpoints
  3. Honey.py spots
    1. Look for genomic variants within the span of reads.
    2. REQUIRED : The MD Tag MUST be present in the bam

Download

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

README

Honey README file

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., Will Salerno, Jeff Reid. 
                                  “PBHoney: Identifying Genomic Variants via
                                  Long-Read Discordance and Interrupted
                                  Mapping."
                                  In Submission
 
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.


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