Open-source alternatives to Bcbio Nextgen

ADAM is a genomics analysis platform with specialized file formats built using Apache Avro, Apache Spark, and Apache Parquet. Apache 2 licensed.

Fast spatial deconvolution via leverage-score sketching — scales to million-spot datasets while preserving rare cell type signals.

Oryx 2: Lambda architecture on Apache Spark, Apache Kafka for real-time large scale machine learning

MONAI is a PyTorch-based deep learning framework and library specifically designed for healthcare imaging. It provides a suite of domain-specific neural network architectures, specialized loss functions, and preprocessing pipelines tailored for analyzing multi-dimensional medical data. The project distinguishes itself through a decentralized federated learning system that allows models to learn from datasets across multiple institutions without exchanging raw patient images. It also features AI-assisted medical image annotation tools and a standardized model bundling system to ensure consiste