PBJelly

This is not official repo. All updates here are for in-house using and no warranty.

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

Requirements

Here listed the tested version.

• python 3.7.3
• networkx 1.7
• blasr 5.3.3

Installation

Using a conda environment is encouraged.

conda create -n PBJelly python blasr
conda activate PBJelly
git clone https://github.com/cgjosephlee/PBJelly
cd PBJelly
python setup.py install

Usage

<stage> is one of

• setup
• mapping
• support
• extraction
• assembly
• output

Jelly.py -h
Jelly.py <stage> -h

Quick start

• Input sequence files must be end with .fasta or .fastq.
• If you are inputing fasta files, use fakeQuals.py to generate dummy quality scores.
• More details in docs/.

Example Protocol.xml:

<jellyProtocol>
    <reference>/FULL/PATH/TO__/PBJelly/data/reference/lambda.fasta</reference>
    <outputDir>/FULL/PATH/TO__/PBJelly/lambdaExample/</outputDir>
    <blasr>--minMatch 8 --sdpTupleSize 8 --minPctIdentity 75 --bestn 1 --nCandidates 10 --maxScore -500 --nproc 8 --noSplitSubreads</blasr>
    <input baseDir="/FULL/PATH/TO__/PBJelly/lambdaExample/data/reads/">
        <job>pacbioReads.fasta</job>
    </input>
</jellyProtocol>

See also docs/TemplateProtocol.xml and docs/jellyExample/Protocol.xml.

Example data:

cd PBJelly/docs/jellyExample
# Edit Protocol.xml according to your path
fakeQuals.py data/reference/lambda.fasta data/reference/lambda.qual
Jelly.py setup Protocol.xml
Jelly.py mapping Protocol.xml
Jelly.py support Protocol.xml
Jelly.py extraction Protocol.xml
Jelly.py assembly Protocol.xml -x "--nproc=8"
Jelly.py output Protocol.xml

Reminder

• Only PBJelly works.
• PBJelly will edit input.fasta and make a backup input.fasta.original, use alias if you feel it's annoying.
• Sometimes it fails without returning error code, go check each xxx.err.