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Error supression and variant calling pipeline for Second-Generation sequencing data

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Dellingr

An error supression and variant calling pipeline for Second-Generation sequencing data

Description

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

Installation

Dependencies

You will need to install the following before installing Dellingr:

  • 3.7>python>=3.4
  • bwa>=0.7.0
  • samtools>=1.3.1

Dellingr will check these dependencies prior to running the pipeline

To install the Dellingr package run the following command:

Install using the Python Package Index (PyPI)

pip install Dellingr

Install from Github

git clone https://github.com/morinlab/Dellingr.git
cd Dellingr
python setup.py install

All required python dependencies will be installed during this step

Running Dellingr

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:

    dellingr run_dellingr -h

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

    /path/to/Dellingr/DellingrPipeline.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:

    dellingr run_dellingr
    -c /path/to/github/clone/etc/dellingr_config.ini

Alternatively:

    /path/to/Dellingr/DellingrPipeline.py 
    -c /path/to/github/clone/etc/dellingr_config.ini

This will run the entire Dellingr 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 ./dellingr_analysis_directory

Helper Scripts

The Dellingr 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:

dellingr -h

dellingr adapter_predict

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

dellingr 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.

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