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ProDuSe

A variant caller designed for use with libraries generated using semi-degenerate barcoded adapters.

Description

See the full wiki page for more information: http://produse.readthedocs.io/en/latest/

Installation

Dependencies

You will need to install the following tools before installing the ProDuSe package:

  • python>=3.5
  • bwa>=0.7.0
  • samtools>=1.3.1

ProDuSe will check that a valid version of these tools are installed prior to running the pipeline

To install the ProDuSe package run the following command:

cd path/to/github/clone/ProDuSe
python setup.py install

All required python dependencies will be installed during this step

Running ProDuSe

The Analysis Pipeline: Very Quick Start

You can view more detailed instructions on the wiki

All parameters required to run ProDuSe can be viewed using the following:

    produse run_produse -h

Alternatively, if you wish to run ProDuSe without installing it, you can run ProdusePipeline.py manually in a similar manner:

    /path/to/ProDuSe/ProdusePipeline.py -h

While these parameters can be specified individually, they can also be provided using a configuration file

To run the analysis pipeline you simply need to run the following command:

    produse run_produse
    -c /path/to/github/clone/etc/produse_config.ini

Alternatively:

    /path/to/ProDuSe/ProdusePipeline.py 
    -c /path/to/github/clone/etc/produse_config.ini

This will run the entire ProDuSe pipeline on all samples specified in the sample_config.ini file, which can be found in etc/sample_config.ini

Results will be located in the following directory:

ls ./produse_analysis_directory

Helper Scripts

The ProDuSe package is comprised of several stages to aid in the analysis of duplex sequencing data.

These stages can be be viewed by running the following:

produse -h

produse adapter_predict

If you need to confirm the expected adapter sequence of a sample you should run the following command:

produse adapter_predict -i input1.fastq input2.fastq

This tool will print a predicted adapter sequence based off of ACGT abundances at each position. It uses these observed abundances and finds the closest expected abundance for an IUPAC unambiguous or ambiguous base.

External links

The Morin Laboratory at SFU