adapter-parser/README.org

• Adapter parser
  • Technologies
  • Installation
  • Usage

Adapter parser

This tool parses fastqc reports to extract the adapter sequences, from the Overrepresented sequences, and then outputs them to a text file. It also outputs the mean and standard deviation of the sequences length.

Technologies

• Pandas

Installation

This project uses Nix to ensure reproducible builds.

1. Install Nix (compatible with MacOS, Linux and WSL):

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

The program expects a folder containing the fastqc reports as an input and an output file where to store the sequences in the FASTA format.

python src/parser.py <input> <output>

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