Dynamic, concurrent, and cache-efficient hash table for streaming k-mer operations

A mapper for 10x-flex single cell sequencing reads with fixed abstract geometries

High-performance cache policies and supporting data structures for Rust systems, with optional metrics and benchmarks.

Fast and Memory Efficient Genome Sketching via HyperLogLog, HyperMinHash and UltraLogLog

A fast and collision resistant hash function for genomics

A hardware-aware guide to data structures for system software engineers.

C++ Genomic Interval B+ Tree Library

Rust library to program hardware performance counter.

Efficient gzip to BGZF transcoder using half-decompression (2-4x faster than decompress+recompress)

A decoder that automatically detects compression format (gzip, bzip2, xz, zstd) via external crates. Includes encoder as well.

Tearing through FASTA/Q sequences

RNA-seq Analysis Pipeline Testing and Optimization Resource - Intelligent pipeline selection and comprehensive benchmarking.

Rust Backend for PyRanges Operations. More featureful and much faster replacement for the NCLS library

Anchor chaining method for nucleotide sequences

Ultra-rapid detection of viral variants directly from sequencing data

Recipes for avoiding bounds checks in Rust, without unsafe!

A small, auxiliary index to massively improve parallel fastq parsing

Benchmark data structures for kmer sets.

A flexible processor for sequencing reads

Quick&dirty MCMF (min-cost-max-flow) implementation using Edmonds-Karp with Dijkstra

Network simplex implementation in Rust

`thaf` is a command-line tool to extract transcript sequences from a genome FASTA file based on GFF3 annotation files. It can also generate transcript-to-gene mapping files compatible with tools su…

More algorithms and utils that work on petgraph graph

min-cost-flow(circulation) with convex cost function on petgraph

ONNX neural network inference engine

A blazingly fast multi-language serialization framework powered by JIT and zero-copy.

A Rust library for the Zarr storage format for multidimensional arrays and metadata

Efficient, parallel compression for terabyte-scale data