GIL: Generate Indexes for Libraries

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.

Installation

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.

Installing from GitHub

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.

Running from a cloned repo

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