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Phylogenetic compression of extremely large genome collections [661k ↘𝟭𝟲𝗚𝗶𝗕 | BIGSIdata ↘𝟰𝟴𝗚𝗶𝗕 | AllTheBact'23 ↘𝟳𝟱𝗚𝗶𝗕]
Slides, paper notes, class notes, blog posts, and research on ML 📉, statistics 📊, and AI 🤖.
Versatile open-source tool for microbiome analysis
QBioCode is a suite of computational resources to support quantum applications in healthcare and life science data.
MCP server for Generating Galaxy Tools
TaGra: TAbular data preprocessing to GRAph representation.
Bracken (Bayesian Reestimation of Abundance with KrakEN) is a highly accurate statistical method that computes the abundance of species in DNA sequences from a metagenomics sample.
upload big files to Zenodo using cURL, jq and bash
List of computational resources for analyzing microbial sequencing data.
Genome modeling and design across all domains of life
Fine-tuning & Reinforcement Learning for LLMs. 🦥 Train OpenAI gpt-oss, DeepSeek-R1, Qwen3, Gemma 3, TTS 2x faster with 70% less VRAM.
An open source deep research clone. AI Agent that reasons large amounts of web data extracted with Firecrawl
Autonomous coding agent right in your IDE, capable of creating/editing files, executing commands, using the browser, and more with your permission every step of the way.
Easily fine-tune, evaluate and deploy gpt-oss, Qwen3, DeepSeek-R1, or any open source LLM / VLM!
A k-mer-based maximum likelihood method for estimating distances of reads to genomes and phylogenetic placement.
Use your android device to boot Linux distributions/ISO files on your PC
A Slurm cluster using docker-compose
This repo collects the list of learning online resources related to microbiome computational science and tools.
ultrafast taxonomic profiling and genome querying for metagenomic samples by abundance-corrected minhash.
HyGen: Compact and Efficient Genome Sketching using Hyperdimensional Vectors
All Algorithms implemented in Python
A tool for drawing ANI clustermap between all-vs-all microbial genomes