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

PGR-TK: Pangenome Research Tool Kit

Phasing reads with secondary alignments

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

Fast and accurate coordinate conversion between assemblies

LongAGE: a memory-efficient implementation of Alignment with Gap Excision (AGE)

Hybrid error correction of long reads using colored de Bruijn graphs

Pipeline to convert a haploid assembly into diploid

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

Open source code for AlphaFold.

WDL’s and Dockerfiles for assembly QC process

GFA insert into GenomicSQLite

GIAB pipeline for benchmarking genome assemblies

the pangenome graph builder

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

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

A genome browser that shows long reads and complex variants better

k-mer based assembly evaluation

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

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

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

Long read / genome alignment software

Raw nanopore signal mapper that enables real-time targeted sequencing

A tool for Racon polishing of miniasm assemblies

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

Validate and edit small eukaryotic genome assemblies