Enabling PyTorch on XLA Devices (e.g. Google TPU)

Super-project for modularized Boost

Fast and accurate coordinate conversion between assemblies

WDL’s and Dockerfiles for assembly QC process

k-mer based assembly evaluation

Open source code for AlphaFold.

The modern C++ library for sequence analysis. Contains version 3 of the library and API docs.

the pangenome graph builder

The Incredible PyTorch: a curated list of tutorials, papers, projects, communities and more relating to PyTorch.

Long read / genome alignment software

Pipeline to convert a haploid assembly into diploid

PGR-TK: Pangenome Research Tool Kit

abPOA: an SIMD-based C library for fast partial order alignment using adaptive band

Phasing reads with secondary alignments

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

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

Raw nanopore signal mapper that enables real-time targeted sequencing

Hybrid error correction of long reads using colored de Bruijn graphs

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

A genome browser that shows long reads and complex variants better

Validate and edit small eukaryotic genome assemblies

Speech Recognition using DeepSpeech2.

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

A faster pytorch implementation of faster r-cnn

Wavefront alignment algorithm (WFA): Fast and exact gap-affine pairwise alignment

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