Daniel E Cook

safetensors. Simple, safe way to store and distribute tensors

polars-bio. Blazing-Fast Bioinformatic Operations on Python DataFrames

deepvariant-linux-arm64. DeepVariant for Linux ARM64 (Graviton, Ampere, RK3588, Jetson) with hardware-accelerated inference via ONNX Runtime + ACL. Open-source variant calling on cheap ARM cloud and edge hardware.

rust-parallel. Fast command line app in rust/tokio to run commands in parallel. Similar interface to GNU parallel or xargs plus useful features. Listed in Awesome Rust utilities.

parallel. This project now lives on in a rewrite at https://gitlab.redox-os.org/redox-os/parallel

nanomix. Python

gbwt-rs. GBZ file format for pangenome graphs

rust-numpy. PyO3-based Rust bindings of the NumPy C-API

vg_wdl. Workflow Description Language (WDL) scripts for common vg workflows

gemini-cli-tips. Gemini CLI Tips and Tricks

command-line-rust. Code for Command-Line Rust (O'Reilly, 2024, ISBN 9781098109417)

multiprocess. better multiprocessing and multithreading in Python

google-cloud-rust. Google Cloud Rust Client Libraries

scientific-agent-skills. Turn any AI agent into an AI Scientist. The #1 Agent Skills library for science, used by 170,000+ scientists worldwide. 158 ready-to-use skills plus 100+ scientific databases covering biology, chemistry, medicine, and drug discovery. Compatible with Cursor, Claude Code, Codex, Pi, Antigravity, and the open Agent Skills standard.

langextract. A Python library for extracting structured information from unstructured text using LLMs with precise source grounding and interactive visualization.

rustworkx. A high performance Python graph library implemented in Rust.

castle. CAncer Standards Long-read Evaluation

heynote. A dedicated scratchpad for power users

bagz. Bagz is a format for storing a sequence of string records. It supports per-record compression and fast index-based lookup.

autogen. Automatically generate boilerplate license comments.

new-project. This repository contains a template you can use to seed a repository for a new open source project.

aardvark. A tool for sniffing out the differences in vari-Ants

python-bigquery-dataframes. This library has moved to https://github.com/googleapis/google-cloud-python/tree/main/packages/bigframes

hmftools. Various algorithms for analysing genomics data

hybrid-boggle. Trying to find the highest-scoring Boggle board with a mix of C++ and Python

arkflow. High performance Rust stream processing engine seamlessly integrates AI capabilities, providing powerful real-time data processing and intelligent analysis.

trgt. Tandem repeat genotyping and visualization from PacBio HiFi data

longcallD. LongcallD: joint calling and phasing of small, structural and mosaic variants from long reads

kalker. Scientific calculator with math syntax that supports user-defined variables and functions, complex numbers, and estimation of derivatives and integrals

haem. A Python library for working on Bioinformatics problems

numbat. A statically typed programming language for scientific computations with first class support for physical dimensions and units

poasta. Fast and exact gap-affine partial order alignment

llama.cpp. LLM inference in C/C++

shaper-origin-inkscape. Inkscape extension to add a Shaper Origin menu to set cut parameters

tensorflow-cmake. Integrate TensorFlow with CMake projects effortlessly

searchless_chess. Grandmaster-Level Chess Without Search

rust-htslib. This library provides HTSlib bindings and a high level Rust API for reading and writing BAM files.

vcfdist. vcfdist: Accurately benchmarking phased variant calls

SVTopo. Complex structural variant visualization for HiFi sequencing data

setuptools-proto. setuptools plugin to compile .proto files using python-betterproto

setuptools-protobuf. protobuf support for setuptools

uv. An extremely fast Python package and project manager, written in Rust.

ccsmeth. Detecting DNA methylation from PacBio CCS reads

Upside-MD. Coarse-grained molecular dynamics for protein physics

alfred-chathub. A chat alfred-workflow that integrates multiple popular large language model (LLM) services, including OpenAI, Anthropic, Gemini, etc

lectures. Material for gpu-mode lectures

GPU-Puzzles. Solve puzzles. Learn CUDA.

positron. Positron, a next-generation data science IDE

flash-linear-attention. 🚀 Efficient implementations for emerging model architectures

FASTGA. Pairwise whole genome aligner

gpu.cpp. A lightweight library for portable low-level GPU computation using WebGPU.

loq. talk to type

warp. A Python framework for GPU-accelerated simulation, robotics, and machine learning.

dlb-kmer-sampling. Optimal distance lower bound k-mer sampling.

concurrentqueue. A fast multi-producer, multi-consumer lock-free concurrent queue for C++11

MuSiCal. A comprehensive toolkit for mutational signature analysis

longcallR. longcallR is a tool for SNP calling, haplotype phasing, and allele-specific analysis with long-read RNA-seq data.

openai-workflow. OpenAI integrations

zenith. Zenith - sort of like top or htop but with zoom-able charts, CPU, GPU, network, and disk usage

annotated_deep_learning_paper_implementations. 🧑‍🏫 60+ Implementations/tutorials of deep learning papers with side-by-side notes 📝; including transformers (original, xl, switch, feedback, vit, ...), optimizers (adam, adabelief, sophia, ...), gans(cyclegan, stylegan2, ...), 🎮 reinforcement learning (ppo, dqn), capsnet, distillation, ... 🧠

vcfpp. a C++ API of htslib to be easily integrated and safely used. More importantly, it can be callled seamlessly in R/Python/Julia etc.

ZLUDA. CUDA on non-NVIDIA GPUs

UsTaxes. Tax filing web application

rapidgzip. Gzip Decompression and Random Access for Modern Multi-Core Machines

llm-app-stack.

deeppolisher. Transformer-based sequence correction method for genome assembly polishing

ngs. Command line utility for working with next-generation sequencing files.

ntHash. Fast hash function for DNA/RNA sequences

quip-sharp. Python

fastfeedforward. A repository for log-time feedforward networks

advent-of-code-cli. A cli tool to automatically download and upload advent of code problems.

machine-learning-articles. 🧠💬 Articles I wrote about machine learning, archived from MachineCurve.com.

pkgx. Run Anything

qsv. Blazing-fast Data-Wrangling toolkit

simple-saca. Hardware go brrr bounded context suffix array construction algorithm

fairseq. Facebook AI Research Sequence-to-Sequence Toolkit written in Python.

deepsomatic. DeepSomatic is an analysis pipeline that uses a deep neural network to call somatic variants from tumor-normal and tumor-only sequencing data.

grain. Library for reading and processing ML training data.

gia. gia: Genomic Interval Arithmetic

google-apis-rs. A binding and CLI generator for all Google APIs

The-Art-of-Linear-Algebra. Graphic notes on Gilbert Strang's "Linear Algebra for Everyone"

hyena-dna. Official implementation for HyenaDNA, a long-range genomic foundation model built with Hyena

flash-attention. Fast and memory-efficient exact attention

rayon. Rayon: A data parallelism library for Rust

grass. Rust

ANTISEQUENCE. Rust library for processing sequencing reads.

hifieval. a tool to evaluate long-read error correction mainly with PacBio High-Fidelity Reads (HiFi reads).

hydro. A Rust framework for correct and performant distributed systems

dynamic-sparse-flash-attention. Jupyter Notebook

Clair. Clair: Exploring the limit of using deep neural network on pileup data for germline variant calling

simde. Implementations of SIMD instruction sets for systems which don't natively support them.

manim. A community-maintained Python framework for creating mathematical animations.

rotary-embedding-torch. Implementation of Rotary Embeddings, from the Roformer paper, in Pytorch

block-aligner. SIMD-accelerated library for computing global and X-drop affine gap penalty sequence-to-sequence or sequence-to-profile alignments using an adaptive block-based algorithm.

alfred-unicode. Preview Unicode characters and emoji in Alfred

google-cloud-rs. Asynchronous Rust bindings for Google Cloud Platform APIs.

fraguracy. overlapping bases in read-pairs from a fragment indicate accuracy and reveal error-prone sites

x-transformers. A concise but complete full-attention transformer with a set of promising experimental features from various papers

strobealign. Aligns short reads using dynamic seed size with strobemers

agc. Assembled Genomes Compressor

local-attention. An implementation of local windowed attention for language modeling

try-manubot. A repository to practice contributing to a Manubot manuscript

coitrees. A very fast interval tree data structure

polars. Extremely fast Query Engine for DataFrames, written in Rust

biodiff. Hex diff viewer using alignment algorithms from biology

generator. A binding and CLI generator for all google APIs

chatgpt-mac. ChatGPT for Mac, living in your menubar.

spacepile. convert reads from repeated measures of same piece of DNA into spaced matricies for deep learners.

BioGPT. Python

From-0-to-Research-Scientist-resources-guide. Detailed and tailored guide for undergraduate students or anybody want to dig deep into the field of AI with solid foundation.

DeepSom. A CNN - based pipeline for calling somatic SNP and INDEL variants without a matched normal

imaginAIry. Pythonic AI generation of images and videos

effective_transformer. Running BERT without Padding

tuning_playbook. A playbook for systematically maximizing the performance of deep learning models.

vision_transformer. Jupyter Notebook

core. :house_with_garden: Open source home automation that puts local control and privacy first.

elevate. A sport app to "Elevate" your training experience and goals! Track your fitness and progressions over time. Analyse deeper your activities. And more...

danielecook.github.io. HTML

best. Bam Error Stats Tool (best): analysis of error types in aligned reads.

clap. A full featured, fast Command Line Argument Parser for Rust

rustlings. :crab: Small exercises to get you used to reading and writing Rust code!

googapis. Rust

SMURF. Python

intel-extension-for-tensorflow. Intel® Extension for TensorFlow*

numerical-linear-algebra. Free online textbook of Jupyter notebooks for fast.ai Computational Linear Algebra course

giremi. GIREMI is a method that can identify RNA editing sites using one RNA-seq data set without requiring genome sequence data.

cramino. A *fast* tool for BAM/CRAM quality evaluation, intended for long reads

Awesome-Diffusion-Models. A collection of resources and papers on Diffusion Models

miniprot. Align proteins to genomes with splicing and frameshift

sd-webui-colab. A repo for the maintenance of the Colab version of stable-diffusion-webui repo

IsoSeq. Iso-Seq - Scalable De Novo Isoform Discovery from Single-Molecule PacBio Reads

boom. bíogo wrapper for libbam - use biogo/hts/bam

tere. Terminal file explorer

psst. Fast and multi-platform Spotify client with native GUI

sv-channels. Deep learning-based structural variant filtering method

tuc. When cut doesn't cut it

highway. Performance-portable, length-agnostic SIMD with runtime dispatch

deNovo-Detect. Perl

EditPredict. Python

gget. 🧬 gget enables efficient querying of genomic reference databases

echtvar. using all the bits for echt rapid variant annotation and filtering

cue. Deep learning framework for SV calling and genotyping

autocomplete. IDE-style autocomplete for your existing terminal & shell

awesome-colab-notebooks. Collection of google colaboratory notebooks for fast and easy experiments

memray. Memray is a memory profiler for Python

still. Unit testing for spreadsheets

alfred-workflow-py3. Full-featured library for writing Alfred 3 & 4 workflows

sklearn-porter. Transpile trained scikit-learn estimators to C, Java, JavaScript and others.

WFA2-lib. WFA-lib: Wavefront alignment algorithm library v2

uBlock-Origin-dev-filter. Filters to block and remove copycat-websites from DuckDuckGo, Google and other search engines. Specific to dev websites like StackOverflow or GitHub.

TetrisJS. This is the classic game of Tetris written in pure HTML

enclone. VDJ Clonotyping & Analysis Tools

awesome-cpp. A curated list of awesome C++ (or C) frameworks, libraries, resources, and shiny things. Inspired by awesome-... stuff.

seqlike. Unified biological sequence manipulation in Python

UMICollapse. Accelerating the deduplication and collapsing process for reads with Unique Molecular Identifiers (UMI). Heavily optimized for scalability and orders of magnitude faster than a previous tool.

ublacklist. Blocks specific sites from appearing in Google search results

haptreex. Haplotype phaser for next-generation sequencing data

hmcnc. Hidden Markov Model based Copy number caller

phaser. phasing and Allele Specific Expression from RNA-seq

diff-align. Differentiable position-specific probability matrix alignment.

vcf-bench. evaluating vcf parsing libraries

clasp. 🔗 Command Line Apps Script Projects

Cogent. Coding Genome Reconstruction using Iso-Seq data

GenomicSQLite. Genomics Extension for SQLite

longbow. Annotation and segmentation of MAS-seq data

redun. Yet another redundant workflow engine

v. Simple, fast, safe, compiled language for developing maintainable software. Compiles itself in <1s with zero library dependencies. Supports automatic C => V translation. https://vlang.io

bam-io-throughput. BAM I/O Throughput Benchmark

cppflow. Run TensorFlow models in C++ without installation and without Bazel

noodles. Bioinformatics I/O libraries in Rust

deepconsensus. DeepConsensus uses gap-aware sequence transformers to correct errors in Pacific Biosciences (PacBio) Circular Consensus Sequencing (CCS) data.

pbcore. A Python library for reading and writing PacBio® data files

rq. Record Query - A tool for doing record analysis and transformation

SmartRNASeqCaller. SmartRNASeqCaller is a post-processing pipeline to improve germline variant calling from RNA-Seq data

conduit. CONDUIT - CONsensus Decomposition Utility In Transcriptome-assembly

XNNPACK. High-efficiency floating-point neural network inference operators for mobile, server, and Web

yak. Yet another k-mer analyzer

panGraphViewer. Show pangenome graphs in an easy way

rclone. "rsync for cloud storage" - Google Drive, S3, Dropbox, Backblaze B2, One Drive, Swift, Hubic, Wasabi, Google Cloud Storage, Azure Blob, Azure Files, Yandex Files

FastAI.jl. Repository of best practices for deep learning in Julia, inspired by fastai

cpsr. Cancer Predisposition Sequencing Reporter (CPSR)

VariantWorks. Deep Learning based variant calling toolkit - https://clara-parabricks.github.io/VariantWorks/

actc. Align subreads to ccs reads

pml-book. "Probabilistic Machine Learning" - a book series by Kevin Murphy

just-the-docs. A modern, high customizable, responsive Jekyll theme for documentation with built-in search.

nushell. A new type of shell

uPlot. 📈 A small, fast chart for time series, lines, areas, ohlc & bars

dsub. Open-source command-line tool to run batch computing tasks and workflows on backend services such as Google Cloud.

rust-mdbg. minimizer-space de Bruijn graphs (mdBG) for whole genome assembly

seqfu2. :rocket: seqfu - Sequece Fastx Utilities

iMessageWrapped. Visualizing and Exploring iMessage data

igv-reports. Python application to generate self-contained pages embedding IGV visualizations, with no dependency on original input files.

perbase. Per-base per-nucleotide depth analysis

rare-disease-wf. (WIP) best-practices workflow for rare disease

quickjs. Public repository of the QuickJS Javascript Engine.

ropebwt2. Incremental construction of FM-index for DNA sequences

genomics-research. Jupyter Notebook

TreeDataOCR. Converts image files to newick notation

tnsv. add true-negative SVs from a population callset to a truth-set.

awesome-bioinformatics-benchmarks. A curated and summarized list of bioinformatics bench-marking papers and resources.