jianshu93

dlb-kmer-sampling

Optimal distance lower bound k-mer sampling.

cudaKDTree

imohash

Fast hashing for large files

minimizers

Measure experimental density of bd-anchors

biotest

Generate random test data for bioinformatics

fastbaps

A fast approximation to a Dirichlet Process Mixture model (DPM) for clustering genetic data

mimalloc_rust

A Rust wrapper over Microsoft's MiMalloc memory allocator

mimalloc

mimalloc is a compact general purpose allocator with excellent performance.

poasta

Fast and exact gap-affine partial order alignment

granges

A Rust library and command line tool for working with genomic ranges and their data.

ndarray-cuda-matmul

a high-performance computing solution designed to accelerate matrix operations using Nvidia's CUDA technology with Rust's ndarray data structure.

gbbs

GBBS: Graph Based Benchmark Suite

SketchNE

Embedding billion-scale networks accurately in one hour (TKDE paper 2023)

graphvite

GraphVite: A General and High-performance Graph Embedding System

DecyclingSetBasedMinimizerOrder

Code and software for minimum-decycling-set-based minimizer orders

fpa

Filter of Pairwise Alignement

ImputeCC

ImputeCC enhances integrative Hi-C-based metagenomic binning through constrained random-walk-based imputation

VilLain

Source code for the paper "VilLain: Hypergraph Embedding with No Labels and No Features via Virtual Label Propagation."

ParlayANN

A library of algorithms for approximate nearest neighbor search in high dimensions, along with a set of useful tools for designing such algorithms.

basic_seed_chainer

evoc

Embedding Vector Oriented Clustering

yacrd

Yet Another Chimeric Read Detector

kraken2-rust

kraken2 rust

anndata-rs

knot

KNOT: Knowledge Network Overlap exTraction is a tool for the investigation of fragmented long read assemblies.

RawHash

RawHash is the first mechanism that can accurately and efficiently map raw nanopore signals to large reference genomes (e.g., a human reference genome) in real-time without using powerful computational resources (e.g., GPUs). Described by Firtina et al. (published at https://academic.oup.com/bioinformatics/article/39/Supplement_1/i297/7210440)

graphest

A faithful graphing calculator

Logan

Logan Unitigs and Contigs

simd-json

Rust port of simdjson

simdjson

Parsing gigabytes of JSON per second : used by Facebook/Meta Velox, the Node.js runtime, ClickHouse, WatermelonDB, Apache Doris, Milvus, StarRocks