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 /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
 
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