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DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.

Official code repository for GATK versions 4 and up

A collaboratively written review paper on deep learning, genomics, and precision medicine

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

Circular visualization in Python (Circos Plot, Chord Diagram, Radar Chart)

Python and C++ code for reading and writing genomics data.

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

Implementation of Enformer, Deepmind's attention network for predicting gene expression, in Pytorch

cython + htslib == fast VCF and BCF processing

? Generative modeling of regulatory DNA sequences with diffusion probabilistic models ?