ScarMapper

A Python-encoded algorithm that uses an iterative break-associated alignment strategy to classify individual double-strand DNA break repair products based on deletion size, microhomology usage, and insertions

Getting Started

These instructions should allow a functional copy of this package to be installed on your local computer. It is highly recomended that you read the user guide before attempting to use this program.

Prerequisites

Linux OS, tested on RHEL 7.x, Scientific Linux 7.x, and CentOS 7.x. Will possibly run on a Mac OS, although it has not been tested. Will not run on Windows because ScarMapper uses Pysam to parse the reference FASTA file.

Minimum System Requirements:
    4 CPUs or threads
    20 Gb RAM
    ~5x the size of the compressed FASTQ file for disk space.

Required Python Libraries:
    Python ≥v3.5, ≥v3.6 recomended
    numpy
    scipy
    python-levenshtein
    python-magic
    natsort
    pathos
    pysam
    cython
    setuptools

Installation

The quickest way to install is to clone or download this repository into a location that accessible to the user. Test installation by moving to the ScarMapper directory and executing python3 scarmapper.py. You should get the error message usage: scarmapper.py [-h] --options_file OPTIONS_FILE scarmapper.py: error: the following arguments are required: --options_file.

Contributing

Pull requests are welcome. For major changes, please open an issue first to discuss what you would like to change.

Please make sure to update tests as appropriate.

Authors

• Dennis Simpson - Initial work

Cite

License

This project is licensed under the MIT License - see the LICENSE file for details