Starred repositories
lite and fast version of just-dna-seq personalized genomic platform
Compress tool outputs, logs, files, and RAG chunks before they reach the LLM. 60-95% fewer tokens, same answers. Library, proxy, MCP server.
Core Hunter 3: a flexible core subset selection tool
Multi-label subcellular localization and sorting signal prediction based on protein foundation models
A pipeline to detect chimeric transcripts derived from genes and transposable elements.
What is true, thank you, ernestly. A large variant benchmarking tool analogous to hap.py for small variants.
A genome language foundation model for microbial genome representation
Software for detecting regions of BrdU and EdU incorporation in Oxford Nanopore reads.
Fast, accurate construction of multiple sequence alignments from protein language embeddings
Tool for identifying the genetic translation table used by prokaryotic organisms
🦖 ClawBio - The first bioinformatics-native AI agent skill library. Local-first. Reproducible. Built on OpenClaw.
A single CLAUDE.md file to improve Claude Code behavior, derived from Andrej Karpathy's observations on LLM coding pitfalls.
KaryoScope: rapid, alignment-free sequence annotation for the pangenome era
Universal Rust multiplexer with a typed SDK — drive any CLI or TUI app from code. Native on Linux, macOS, and Windows.
One liner tool to check the quality of your single-cell atlases.
A deterministic, low-memory genomics engine in Rust — run whole-genome workloads on your laptop. Declare your RAM, get a verifiable receipt, and reproduce results byte-for-byte.
A fast terminal Excel viewer with an interactive TUI. Features full-text search, formula display, lazy loading for large files, clipboard support, and export to CSV/JSON. Built with Rust and ratatui.
Genotype Inference using Genome Graphs and Long rEadS (Giggles)
An extensible and performant aligner and read mapper
Pre-indexed code knowledge graph, auto syncs on code changes, for Claude Code, Codex, Gemini, Cursor, OpenCode, AntiGravity, Kiro, and Hermes Agent — fewer tokens, fewer tool calls, 100% local