Addgene is a nonprofit organization whose mission is to accelerate research and discovery by improving access to useful research materials and information. Since the company was founded in 2004, scientists have shared more than 100,000 unique published reagent samples via Addgene’s repository. We have also fulfilled requests for more than 1.5 million plasmid, viral vector, and other material types to scientists in 100+ countries.
Addgene conducts a rigorous quality control process for all plasmids and viral vectors we distribute. Part of this quality control involves sequencing the materials using Next Generation Sequencing (NGS). As our NGS data volume grows, we have had to find ways to automate many parts of our analysis. We do so through internally developed bioinformatics tools. Our language of choice is Python 3.
The aim of this code repository is to make these tools available to the broader scientific community. Stay tuned as the Addgene Toolkit grows!
Prerequisites
Terminal application
You will need to use a Terminal application to launch toolkit commands (either natively or via our docker container).
If you’re on a Mac, The Terminal app can be launched by going to Applications > Utilities and double clicking on
Terminal.
We suggest adding this application to your Dock. The commands that you need to type in the Terminal window are in this
font.
- Cheat sheet for the Mac Terminal app:
- Use TAB to complete a command or file name after typing a few letters.
- Hit ENTER to execute the command.
- Use Ctrl-C to interrupt a command.
- Use the Up arrow to get to the previously typed commands.
Python environment
First of all download the
addgene/openbio zipfile, move it to your Home folder, and expand it.
If you already have a Python 3 environment of your liking, you simply need to navigate to the openbio-main root,
issue the command:
pip install -r requirements.txt
and move on.
If you don’t already have a Python environment, you may use our Docker container, which includes everything you need to use the toolkit. Please visit this page to learn how to build and use it.
The Addgene Toolkit
Basics
The entry point to the Addgene Toolkit is the command atk.
In a terminal window, navigate to the toolkit folder (if you’re using our Docker container, run the
container first):
cd openbio-main/toolkit
Run atk as follows to learn more:
python atk.py --help
This lists the tools that are available as commands and their parameters. The general pattern to invoke a command is:
python atk.py [command]
Commands
- Serotypes - detect and report specific signatures in NGS data, useful to differentiate viral serotypes.
- Recombination - detect recombination in NGS data, used for Cre-Lox quality control.