Interactive, browser-based viewer for HPRC pangenome graphs at the locus level

Snap alignments to query exon boundaries

A library for easy, fast, and efficient reading & writing of PLINK Bed files

Rust reimplementation of the GATK4 HaplotypeCaller germline short-variant spine (HC → CombineGVCFs → GenotypeGVCFs → hard-filter VariantFiltration).

Accelerated short-read alignment, derived from bwa-mem2 — drop-in replacement with correctness fixes, performance improvements, single-binary methylation, and shared-memory index.

Prediction of NB-LRR resistance genes based on full-length sequence homology

To use Evo2 easily

A framework for state-of-the-art pre-trained bio foundation models on genomics and transcriptomics modalities.

Rust port of gfa-to-pairwise-paf: pairwise PAF unpacked from a pangenome graph's GFA, byte-identical to the Python tool

PhotoCraft: An open-source, photo editor written by scratch in pure Rust

Define durable workflows in YAML, powered by Temporal

Haplotype-Aware Structural Variant Detector

Pangenome-based structural variation caller

Paludamentum is the coat of the emperor - evidence processing pipeline

Ecosystem of libraries and tools for writing and executing fast GPU code fully in Rust.

POOCH is a Snakemake-based pipeline for assigning chromosome labels and determining the parent of origin (maternal or paternal) of near-complete genome assemblies.

Variant (SNV and small indel) calling from ONT sequencing data on the mitochondria

A nucleotide-level pangenome simulator.

gemsparcl 💎✨ Rapid and consistent clustering of millions of genomes highlights the diversity of prokaryotic life

A suite of C++ programs developed for transposable element search and their annotation in large eukaryotic genome sequence. A part of the REPET package.

A collection of AI contribution policies which can be copied into other projects.

Extract clipped alignment

tree visualization for tree + annotation data

Unsupervised Deep Gene Finding

Fast, highly accurate, read-trimming for NGS data.

Managing sequencing data with RDF

A streaming, record-aware splitter and converter for the everyday sequence and alignment formats.