adapter-parser/README.org

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* 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 [[https://nixos.org][Nix]] to ensure reproducible
builds.
1. Install Nix (compatible with MacOS, Linux and
[[https://docs.microsoft.com/en-us/windows/wsl/about][WSL]]):
#+begin_src bash
curl -L https://nixos.org/nix/install | sh
#+end_src
2. Clone the repository:
#+begin_src bash
git clone https://git.coolneng.duckdns.org/coolneng/adapter-parser
#+end_src
3. Change the working directory to the project:
#+begin_src bash
cd adapter-parser
#+end_src
4. Enter the nix-shell:
#+begin_src bash
nix-shell
#+end_src
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.
#+begin_src bash
python src/parser.py <input> <output>
#+end_src
#+RESULTS:
:
: 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