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Source code related to the publication "Visualization of loop extrusion by DNA nanoscale tracing in single human cells" by Beckwith, Ødegård-Fougner et.al. DOI: https://doi.org/10.1101/2021.04.12.439407

The Bretzel app's front-end code.

Deployment configuration for the Bretzel App project.

The back-end API.

PyO3 bindings and Python interface to skani, a method for fast fast genomic identity calculation using sparse chaining.

Cython bindings and Python interface to FastANI, a method for fast whole-genome similarity estimation.

SVLT = Serving Vision to Living Things. A service for on-demand computer vision, targeted at image feedback in microscopy and other life sciences applications.

Server to implement image analysis jobs for online use (e.g. in feedback microscopy), including adapters to ilastik and TensorFlow.

Python interface to Prodigal, an ORF finder for genomes, progenomes and metagenomes.

Cython bindings and Python interface to HMMER3.

Cython bindings and Python interface to SWORD (Smith Waterman On Reduced Database), a method for fast database search.

A Python interface to gb-io, a fast GenBank parser and serializer written in Rust.