Grapple is a small Python script intended to allow users to create consensus genomes from unpaired NGS reads. Grapple utilizes common bioinformatics tools such as samtools and bowtie2 in order to pipeline the inputted NGS reads into a consensus FASTA file.
Grapple was developed using Python 2.7 on OS X. However, it will likely work with little to no modification on other platforms with other Python runtimes (including Python 3 runtimes). The main requirements for the script to execute are its dependencies (enumerated below).
To run Grapple, clone this repository and run the main script grapple.py. You will need to install Grapple's dependencies from PyPI before the script can be used. Try the command:
sudo pip install -r requirements.txt
Grapple also requires the following utilities to be installed and in your PATH:
- samtools
- karect
- bowtie2
- bcftools
If you would like to automate the installation of Grapple, a Homebrew formula is available. Try the following commands:
brew tap qsirianni/bioinformatics
brew install grapple