Nextflow pipeline for Twist Comprehensive Genomic Profiling (CGP) panel analysis

FinaleToolkit is a package and standalone program to extract fragmentation features of cell-free DNA from paired-end sequencing data.

Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)

Collection of bioinformatics-related WDL modules and pipelines

Accelerated genomics workflows in the Workflow Description Language (fork: see NVIDIA repo for official version)

Free Accounting Software

tiktoken is a fast BPE tokeniser for use with OpenAI's models.

Infinity is a high-throughput, low-latency serving engine for text-embeddings, reranking models, clip, clap and colpali

Next-Gen Big Data File Format

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

MMseqs2: ultra fast and sensitive search and clustering suite

Learn to analyse genomics data from cancer samples with hands-on practical exercises in mutation calling, driver gene identification, mutational signature analysis and RNA deconvolution.

BioNeMo Framework: For building and adapting AI models in drug discovery at scale

LLM training in simple, raw C/CUDA

PDBFixer fixes problems in PDB files

Open source code for AlphaFold.

Mamba SSM architecture

A set of examples around pytorch in Vision, Text, Reinforcement Learning, etc.

1️⃣🐝🏎️ The One Billion Row Challenge -- A fun exploration of how quickly 1B rows from a text file can be aggregated with Java

Pipeline to calculate de novo mutation rates from parent-offspring trios

Official code repository for GATK versions 4 and up