Using PBHoney

PBhoney is a tool to use mapped long reads (PacBio) to look for genomic variants.

Publication
Software

Setting up your environment:

module load python2/2.7.3
. /projects/cees/src/env_pbjelly/151203_pbhoney/bin/activate
export PYTHONPATH=/projects/cees/src/env_pbjelly/151203_pbhoney/lib/python2.7/site-packages:$PYTHONPATH
module load samtools/1.1 smrtanalysis/2.3.0
source /projects/cees/bin/pbjelly/20150413/pb-jelly-code-0/setup.sh

Test if the program runs:

Honey.py -h

There is an example dataset in the installation in docs/honeyExample/, to use:

cd somefolder
cp /projects/cees/bin/pbjelly/20150413/pb-jelly-code-0/docs/honeyExample/filtered_subreads.fastq .
cp /projects/cees/bin/pbjelly/20150413/pb-jelly-code-0/docs/honeyExample/lambda_modified.fasta .

inputReads=filtered_subreads.fastq
reference=lambda_modified.fasta

# Mapping
Honey.py pie $inputReads $reference

# sam to bam
sam2bam $reference filtered_subreads.tails.sam

# calling tails
Honey.py tails filtered_subreads.tails.bam

# calling spots
Honey.py spots filtered_subreads.tails.bam --reference $reference

Output files: filtered_subreads.tails.hon.tails and filtered_subreads.tails.hon.spots.