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README.org

Adapter parser

This tool parses fastqc reports to extract the adapter sequences, from the Overrepresented sequences, and then outputs them to a text file.

Technologies

  • Pandas

Installation

This project uses [Nix](https://nixos.org/) to ensure reproducible builds.

  1. Install Nix (compatible with MacOS, Linux and [WSL](https://docs.microsoft.com/en-us/windows/wsl/about)):
curl -L https://nixos.org/nix/install | sh
  1. Clone the repository:
git clone https://git.coolneng.duckdns.org/coolneng/adapter-parser
  1. Change the working directory to the project:
cd adapter-parser
  1. Enter the nix-shell:
nix-shell

After running these commands, you will find yourself in a shell that contains all the needed dependencies.

Usage 

python src/parser.py -h

\[\] usage: parser.py [-h] input output

positional arguments:
  input       directory containing the fastqc reports
  output      file where to export the sequences

optional arguments:
  -h, --help  show this help message and exit