Getting Started

To install with pip:

$ pip install swiftseq

Or to get the latest development version:

$ pip install git+


The development version may not be stable

Once SwiftSeq is install, software dependencies can be installed with Bioconda:

$ swiftseq install-env

This will produce an executables.config file that the user can pass directly into a SwiftSeq run.


The above command will only work if the user has Anaconda/Miniconda installed. It’s provided as a convenience; if the user would rather install software dependencies manually, Swiftseq only needs an executables.config at runtime and is indifferent to where it comes from.

The user can then run Swiftseq:

swiftseq run --exe-config /path/to/executables.config [options]