GIL is a Python package that designs indexing primers for multiplexed sequencing.
See the wiki for explanations of what GIL does and examples of how to use it. Can't find an answer to your question in the wiki? Start a discussion on GIL's discussion page.
Want a feature added to GIL? Make a feature request on the issues page.
A web app version of GIL is available here: https://dbl-gil.streamlitapp.com/. If you encounter a message saying the app is down/booting, please be patient and try again in 30 minutes. This can happen due to inactivitiy.
GIL requires Python 3.6 or higher and is not compatible with Python 2. The optional
Levenshtein module (pip install Levenshtein) makes index generation much faster but is not required.
To install GIL from GitHub, use
pip install git+https://github.com/de-Boer-Lab/GIL
GIL can then be run as follows:
GIL [COMMAND] [ARGUMENTS]
For help:
GIL -h
or
GIL [COMMAND] -h
See usage examples below for more details, and the command line arguments section for explanations of all arguments.
If you'd prefer not to install GIL, you can instead clone the repo:
git clone https://github.com/de-Boer-Lab/GIL.git
Commands can only be run from the top-level GIL directory as follows:
python -m GIL.[COMMAND] [ARGUMENTS]
For example, to generate indexes of length 10, run
python -m GIL.generate_indexes --length 10