A terminal UI for monitoring Snakemake workflows

snakemake grammar for tree-sitter, based on tree-sitter-python

About SciPy 2026 tutorial on "Reproducible CUDA Accelerated Workflows for Scientists with Pixi"

CUDASW++4.0: Ultra-fast GPU-based Smith-Waterman Protein Sequence Database Search

gpuPairHMM: Ultra-fast GPU-based PairHMM for DNA Variant Calling

Pydantic-backed validation of delimited text files.

Tools for fiberseq data written in rust.

Simple creation of data classes from dictionaries.

CV/resume generator for academics and engineers, YAML to PDF

Apache OpenDAL: One Layer, All Storage.

Programming for Biology @ CSHL 2025

Visualise networks and trees in Python, with style.

Up to 100x faster strings for C, C++, CUDA, Python, Rust, Swift, JS, & Go, leveraging NEON, AVX2, AVX-512, SVE, GPGPU, & SWAR to accelerate search, hashing, sorting, edit distances, sketches, and m…

Exploratory data analysis of d4 coverage files

A Python library for processing genomes with ease

marimo + pixi starter template

Real time monitor for snakemake

Chrome extension to automatically export UCD Schedule Builder Calendars to Google Calendar

Generate kmers/minimizers/hashes/MinHash signatures, including with multiple kmer sizes.

Guide to p4lang repositories and some other public info about P4

Viral genome alignment, clade assignment, mutation calling, and quality checks

Short snippets of useful code (mostly comp bio stuff)

docs holder for usher wiki

A phylogeny dating method using least-squares algorithms and criteria

Cython API for the Mutation Annotated Tree (MAT) Online Phylogenetics Toolkit (In Development)