kmermaid is a Python3.8+ package containing tools for extraction of k-mers from an input sequence. Furthermore, it can count the sequences or extract only unique sequences. The approach of kmermaid is a straightforward n-way join of batches of k-mers, thus alleviating the toll that similar tools can exhert on memory while requiring fast I/O speeds on disk (SSDs are recommended). Read the online documentation for more details.
kmermaid is fully implemented in Python3.8+, thus you need the corresponding Python version to run it. Check out here how to install Python+ on your machine if you don't have it yet.
kmermaid has been tested with Python 3.8 and 3.9. We recommend installing it using pipx (see below) to avoid dependency conflicts with other packages. The packages it depends on are listed in our dependency graph. We use poetry to handle our dependencies.
We recommend installing kmermaid using pipx. Check how to install pipx here if you don't have it yet!
Once you have pipx ready on your system, install the latest stable release of kmermaid by running: pipx install kmermaid. If you see the stars (✨ 🌟 ✨), then the installation went well!
All kmermaid commands are accessible via the kmer keyword on the terminal. For each command, you can access its help page by using the -h option. More details on how to run kmermaid are available in the online documentation.
We welcome any contributions to kmermaid. In short, we use black to standardize code format. Any code change also needs to pass mypy checks. For more details, please refer to our contribution guidelines if this is your first time contributing! Also, check out our code of conduct.
MIT License - Copyright (c) 2017-2021 Gabriele Girelli