FMSI is a highly memory efficient exact k-mer set based on masked superstrings and the masked Burrows-Wheeler transform

Perfect hashing for an imperfect world

Succinct Data Structure Library 3.0

Comparison of different MPHF algorithms

A high performence Cross-platform (parallel) STL-like LSD radix sort algorithm by C++20, 2.5-14.3x faster than std::sort, support user-defined struct.

A k-mer search engine for all Sequence Read Archive public accessions

Rust porting of the WebGraph and Zuckerli graph compression frameworks

Library for writing Reduced Alignment Data (RAD) format files.

An ancient lightweight Suffix Array and BWT construction algorithm

BWT construction and search

What should perfect bioinformatic tools be like?

Approximate nearest neighbour search for microbial genomes based on hash metric

Cute tricks for SIMD vectorized binary encoding and decoding of nucleotides, in Rust.

Rust rewrite of SSHash

Fulgor is a fast and space-efficient colored de Bruijn graph index.

Metabuli: specific and sensitive metagenomic classification via joint analysis of DNA and amino acid.

Official software repository of S. Bruch, F. M. Nardini, C. Rulli, and R. Venturini, "Efficient Inverted Indexes for Approximate Retrieval over Learned Sparse Representations". Long Paper @ ACM SIG…

Iterate over minimizers of a DNA sequence

The book "Performance Analysis and Tuning on Modern CPU"

Reference implementations of minimizer schemes to go with the mod-minimizers paper.

High throughput suffix array searching

A modular, reusable university course for Rust

Optimal distance lower bound k-mer sampling.

A comparative, extendable benchmarking suite for C and C++ hash-table libraries.

Classifier for metagenomic sequences using FM-index with run-block compressed BWT.

Mumemto: multi-MUM and MEM finding across pangenomes

Benchmarks of Kaminari competitors

A catalogue of Rust design patterns, anti-patterns and idioms