FDSTools User Guide
Please note: the FDSTools User Guide is still a work in progress. For now, you will find a brief introduction and installation instructions on this page. The complete guide will be available here soon.
1. Introduction: What is FDSTools?
FDSTools is a package of data analysis tools for Massively Parallel Sequencing (MPS, also known as Next Generation Sequencing or NGS) of forensic DNA markers. It includes tools for characterisation and filtering of PCR stutter artefacts and other systemic noise, and for automatic detection of the alleles in a sample.
The package was created by Jerry Hoogenboom in 2016 as the product of his MSc Bioinformatics thesis project, at the LUMC (Leiden, the Netherlands). Development is continued at the NFI (The Hague, the Netherlands).
FDSTools is a collection of many command-line tools which can either be used separately or by using one of the built-in pipeline options. Results are visualised in the form of web pages (HTML files) in which various analysis settings can still be tweaked. In this User Guide, you will get to know the most important tools and visualisations and the pipeline options. A complete description of all tools and options can be found on the Tools page, or through the built-in help (command: fdstools --help).
2. Installing FDSTools
FDSTools is written in Python, so you need to have Python installed on your system first. Get it from Python.org if you are on Windows. MacOS and most Linux systems come with Python preinstalled. Currently, FDSTools requires Python 2.7 and will not work with Python 3.
There are two ways to install FDSTools: you can use the Python package installer programme pip, or install FDSTools manually.
Installing FDSTools through pip
The easiest way to install FDSTools is by using the command pip install fdstools. This will automatically download and install FDSTools on your system. This command uses the pip programme, which is bundled with the Python installer for Windows. On Linux, you can install pip using the system's package management tools (e.g., on Ubuntu, apt install python-pip). On MacOS, you can get pip with the command easy_install pip.
Updating FDSTools (as well as any other Python package) to the latest version is also very easy with pip. Just run the command pip install --upgrade fdstools and you're done.
Installing FDSTools manually
If you can't (or don't want to) use pip, it is also possible to install FDSTools manually. The latest stable version can be downloaded from the Python Package Index (PyPI). Unzip the package you downloaded from that site, and then run python setup.py install to set it up.