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nucleo-matcher
plug and play high performance fuzzy matcher
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fuzzy-matcher
Fuzzy Matching Library
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foyer
Hybrid cache for Rust
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bio
A bioinformatics library for Rust. This library provides implementations of many algorithms and data structures that are useful for bioinformatics, but also in other fields.
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musli-zerocopy
Refreshingly simple zero copy primitives by Müsli
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egui_graphs
Interactive graph visualization widget for rust powered by egui
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blutils-cli
The CLI port of the blutils library
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stringzilla
Search, hash, sort, fingerprint, and fuzzy-match strings faster via SWAR, SIMD, and GPGPU
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bio-seq
Bit packed and well-typed biological sequences
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bnf
parsing Backus–Naur form context-free grammars
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bitnuc
efficient nucleotide sequence manipulation using 2-bit and 4-bit encodings
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xan
The CSV magician
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codebook
A code-aware spell checker library (dependency for codebook-lsp)
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gsearch
genome classification, probminhash hnsw, genome search
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generic_a_star
A generic implementation of the A* algorithm
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plascad
PlasCAD
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hctr2-rs
HCTR2 and HCTR3 length-preserving encryption with format-preserving variants
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kira-qc
FastQC-compatible QC tool written in Rust
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wind_tunnel_instruments
Instruments for measuring performance with Wind Tunnel
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grepq
quickly filter fastq files
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bio_files
Save and load common biology file formats
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hashfasta
Very quickly compute hashes for FASTA/FASTQ files considering only the sequence content
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bqtools
A command-line tool for interacting with BINSEQ file formats
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packed-seq
Constructing and iterating packed DNA sequences using SIMD
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simd-minimizers
A SIMD-accelerated library to compute random minimizers
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base-d
Universal base encoder: Encode binary data to 33+ dictionaries including RFC standards, hieroglyphs, emoji, and more
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predictosaurus
Uncertainty aware haplotype based genomic variant effect prediction
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lightmotif
A lightweight platform-accelerated library for biological motif scanning using position weight matrices
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primerpincer
A CLI primer trimming tool for long-read sequencing data
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symspell_rs
Spelling correction & Fuzzy search
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zoe
A nightly library for viral genomics
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seqhash
Fast mismatch-tolerant sequence lookup with disambiguation
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dynamics
Molecular dynamics
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vsf
Versatile Storage Format
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sassy
Approximate string matching using SIMD
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block-aligner
SIMD-accelerated library for computing global and X-drop affine gap penalty sequence-to-sequence or sequence-to-profile alignments using an adaptive block-based algorithm
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quadrank
Fast rank over binary and size-4 DNA alphabets
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simdna
High-performance SIMD-accelerated DNA sequence encoding supporting all IUPAC nucleotide codes
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biometal
ARM-native bioinformatics library with streaming architecture and evidence-based optimization
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sufr
Parallel Construction of Suffix Arrays in Rust
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barbell
Extremely fast and accurate Nanopore demultiplexing
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micro-hnsw-wasm
Neuromorphic HNSW vector search with spiking neural networks - 11.8KB WASM for edge AI, ASIC, and embedded systems. Features LIF neurons, STDP learning, winner-take-all, dendritic computation.
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rhmm
hidden markov models
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segul
An ultrafast and memory-efficient tool for phylogenomics
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karma
A sophisticated Hidden Markov Model (HMM) implementation using the Baum-Welch algorithm
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kmerutils
Kmer counting, hashing, sequence sketching
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toml-pretty-deser
TOML deserilization with pretty error messages
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seqkmer
High-performance FASTA/FASTQ IO and minimizer-based k-mer analysis utilities for Rust bioinformatics pipelines
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kmerust
A fast, parallel k-mer counter for DNA sequences in FASTA and FASTQ files
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lightmotif-py
PyO3 bindings and Python interface to the lightmotif crate
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nucs
working with nucleotide and amino acid sequences
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shah
custom database
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iirs
Inverted repeats finder
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sourmash
tools for comparing biological sequences with k-mer sketches
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fastqgen
Random paired fastq file generation. Nothing more, nothing less.
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genetic_algorithms
solving genetic algorithm problems
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kira-biodata-manager
Reproducible bio-data manager with a project-local store and a shared global cache. kira-bm it's like npm/cargo/pip for bioinformatics.
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binseq
A high efficiency binary format for sequencing data
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lib_ts_chainalign
A chaining-based sequence-to-sequence aligner that accounts for template switches
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na_seq
DNA, RNA, and amino acid sequence types and functions
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mbf-fastq-processor
The fast, reliable multitool of FASTQ processing
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hmm_tblout
Parse nhmmer tblout files
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deacon
Fast DNA search and [host] depletion using minimizers
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microBioRust
Microbiology friendly bioinformatics Rust functions
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tidk
A toolkit for finding telomeric repeats in a genome
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nafcodec
Rust coder/decoder for Nucleotide Archive Format (NAF) files
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dnacomb
Count the occurances of structured sequence reads and compare to an expected library
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lightmotif-tfmpvalue
Rust reimplementation of TFMPvalue for the lightmotif crate
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tsalign
A sequence-to-sequence aligner that accounts for template switches
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d4-framefile
The Framefile container crate for D4 file format
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moma
Moving Origin Modular Arithmetic (MOMA), a library for modeling complex systems
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fakit
program for fasta file manipulation
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selexqc
High-performance parallel RNA Capture-SELEX library quality control
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gb-io
parsing, writing and manipulating Genbank sequence files
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ska
Split k-mer analysis
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odgi-ffi
A safe, ergonomic Rust wrapper for the odgi pangenome graph tool
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mappy-core
Core maplet data structure implementation
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fibertools-rs
Fiber-seq toolkit in rust
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salti
A modern, fast, multiple sequence alignment browser - built for the terminal
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hashirama
Gemini ai based CLI in the taste of Hashirama Senju
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seal
Needleman-Wunsch & Smith-Waterman sequence alignment
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biodiff
Compare binary files using sequence alignment
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symbios-genetics
Sovereign biology engine for Quality-Diversity and Multi-Objective evolution
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fxread
A barebones fastx reader for rust
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seq-hash
A SIMD-accelerated library to compute hashes of DNA sequences
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rdx-stderr
The Rustadex Stderr Package. An opinionated, ergonomic library for pretty-okay CLI terminal output, made of sticks bubble gum and vintage bash scripts.
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jamhash
A fast, simple hash function with dual-path accumulation
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rvdna
— AI-native genomic analysis and the .rvdna file format. Variant calling, protein prediction, and HNSW vector search in pure Rust with WASM support.
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nanalogue
BAM/Mod BAM parsing and analysis tool with a single-molecule focus
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redicat
RNA Editing Cellular Assessment Toolkit: A highly parallelized utility for analyzing RNA editing events in single-cell RNA-seq data
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bio_apis
DNA and RNA sequence types and functions
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synthdb
The Universal Database Seeder. Production-grade synthetic data generator for PostgreSQL. Zero config, context-aware.
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orphos-core
Core library for Orphos, a tool for finding protein-coding genes in microbial genomes
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bio-types
A collection of common biomedical types for use in rust-bio and rust-htslib
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thaf
Extracts transcript sequences and gene maps from genome FASTA files using GFF3 annotations
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raxtax
k-mer-based non-Bayesian Taxonomic Classifier
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par-particle-life
GPU-accelerated particle life simulation in Rust
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nthash-rs
Pure‑Rust port of ntHash
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nucleaze
Read filtering using k-mers
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photodna
Safe, high-level Rust bindings for the Microsoft PhotoDNA Edge Hash Generator
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kira-ls-aligner
Unified short- and long-read sequence aligner written in Rust 2024. It combines minimap2-style minimizers and chaining with BWA-MEM2-style exact-match anchoring and output semantics…
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simd-sketch
A SIMD-accelerated library to compute a b-bit bottom-h sketch
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seven-layer-symphony
Death of code, birth of music. Time-weaving consciousness system where intent manifests reality through 7-dimensional resonance at 432Hz
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bnf_sampler
that uses recursive descent algorithm to ensure tokens produced by a large language model follow a Backus Naur Form schema
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genedex
A small and fast FM-Index implementation
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sigil-parser
Parser and native compiler for the Sigil programming language
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chip_as_code
Semantic Chips — deterministic boolean circuits as text DNA. Parse, evaluate, evolve, and prove policy gates with No-Guess constitutional checkpoints.
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fuzzy_rocks
A persistent datastore backed by RocksDB with fuzzy key lookup using an arbitrary distance function accelerated by the SymSpell algorithm
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methyltracer-cli
Universal adapter for DNA methylation data formats
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funutd
Procedural texture library
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coverm
Read coverage calculator for metagenomics
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bsxplorer2
A high-performance library for bisulfite sequencing data analysis and DNA methylation research
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ffcharge
A lightweight pure Rust library for fast, residue-based force field charge assignment (AMBER/CHARMM) in molecular modeling pipelines
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stats_on_gff3
Calculate statistics such as CDS GC3 ratio, intron GC ratio, flanking gene region GC ratio, first intron length, number of introns, CpG ratio, etc. Examples: stats_on_gff3 Homo_sapiens…
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d4-bigwig
The libBigWig binding used by D4
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qslib
QuantStudio qPCR machine library
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cell-cli
Cargo-installable CLI for Cell ‑ 48 Gbps zero-copy RPC services
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rusty-dna
Normalize consumer DNA genotype exports into structured SNP data via provider-specific parsers
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genesis-protocol
🧬 The first protocol for digital life - creating, evolving, and networking living digital organisms
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base_sequence_compression
compressing and decompressing DNA sequences
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onecode
Rust bindings for ONEcode - a data representation format for genomic data
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fuzzyfold
Nucleic acid secondary structure kinetics
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elid
A fast and efficient string similarity library
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sbwt
Indexing sets of DNA k-mers with the spectral Burrow-Wheeler transform
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genomicsqlite
Genomics Extension for SQLite
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mini_myers
SIMD myers for short queries
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nucleob
bioinformatics: nucleobases and amino acids statistics
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groan_rs
Gromacs Analysis Library for Rust
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gskits
common kits
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libsufr
Parallel Construction of Suffix Arrays in Rust
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disambiseq
Create unambiguous one-off mismatch libraries for DNA sequences
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umgap
The Unipept Metagenomics Analysis Pipeline
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minimizer-iter
Iterate over minimizers of a DNA sequence
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d4tools
The CLI utils for D4 file format
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blutils-proc-adapter
easier to run and analyze Blast results
-
barcode-count
NGS barcode counter for DEL, CRISPR-seq, and Barcode-seq
-
neat
working with NEAT in rust
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awry
creating FM-indexes from FASTA/FASTQ files. AWRY is able to search at lightning speed by leveraging SIMD vectorization and multithreading over collections of queries.
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suffix
arrays
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oxirs-stream
Real-time streaming support with Kafka/NATS/MQTT/OPC-UA I/O, RDF Patch, and SPARQL Update delta
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epimetheus-methylome
DNA motif representation and methylation analysis, supporting IUPAC codes and Nanopore methylation data (6mA, 5mC, 4mC)
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rustome
Genetic tools
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codenano
editing DNA molecular designs
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ff_structure
fuzzyfold's secondary structure representations
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quad-fm
Fast count-only FM-index size-4 DNA alphabets
-
skani
fast tool for calculating ANI between metagenomic sequences, such as metagenome-assembled genomes (MAGs). It is extremely fast and is robust against incompleteness and fragmentation, giving accurate ANI estimates.
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cigar-lodhi-rs
Lodhi subsequence kernel on CIGAR strings
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debruijn
Tools for DNA sequences: efficient k-mer manipulation, De Bruijn graph construction and compaction and handling of DNA strings
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blend_info
Print some information about a Blender scene file
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codenano-server
editing DNA molecular designs in a browser
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pseqsid
Calculates pairwise sequence identity, similarity and normalized similarity score of proteins in a multiple sequence alignment
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med-bed
Digital MedBed protocol - heal consciousness by replacing dissonant genes with resonant ones
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nom-pdb
PDB parser implemented with nom
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codonrs
Calculate relative synonymous codon usage for coding DNA sequences in a fasta file
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bsxplorer-ci
A high-performance tool for bisulfite sequencing data analysis and DNA methylation research
-
omics
Foundations for omics analysis using Rust
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frag_gene_scan_rs
gene prediction model for short and error-prone reads
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ff_energy
fuzzyfold's nearest neighbor free energy evaluations
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classeq-cli
A command line interface for the classeq library
-
microBioRust-seqmetrics
Microbiology friendly bioinformatics Rust functions
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nafcodec-py
PyO3 bindings and Python interface to the nafcodec crate
-
flame-clustering
Fuzzy clustering by Local Approximation of MEmberships (FLAME)
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bio-streams
Streaming bioinformatics data types
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lightdock
Macromolecular docking software based on the GSO algorithm
-
nthash
rolling hash function for hashing all possible k-mers in a DNA sequence
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spikeq
A synthetic FASTQ record generator with pattern spiking
-
motif-scanner
Command line tool for scanning DNA sequences for transcription factor binding sites
-
photodna-sys
Low-level FFI bindings to the Microsoft PhotoDNA Edge Hash Generator library
-
libsfasta
Better FASTA sequence compression and querying
-
ff_kinetics
fuzzyfold's stochastic secondary structure simulations
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sigalign-utils
utils for core
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diploid-contam-estimator
Estimating contamination level in diploid DNA seuqencing libraries
-
tf-binding-rs
Fast transcription factor binding site prediction and FASTA manipulation in Rust
-
gen
A sequence graph and version control system
-
holo_hash
hashing helpers supporting dht sharding
-
fastq-generator
A fastq generator for generation of synthetic fastq files
-
hdk
The Holochain HDK
-
flowtigs
An algorithm for calculating flowtigs in a De Bruijn graph of DNA reads in metagenomes
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karyon_net
Internal crate for Karyon library
-
handlegraph
in variation graphs
-
aaa
CLI tool for work with 3a files
-
partialdebug
Derive Debug partially
-
blutils-core
easier to run and analyze Blast results
-
snatch
fast download accelerator
-
hdi
The HDI
-
strobemers-rs
strobemers
-
cadnano-format
An interface to the format used by Cadnano to represent DNA Origami designs
-
protein-translate
Translate nucleotide sequence to protein
-
jean_blosum
BLOSUM feature for jean
-
omics-variation
Foundational representations of variation in the Rust omics ecosystem
-
holochain_zome_types
Holochain zome types
-
biogarden
A collection of basic bioinformatics algorithms
-
cainome
Generate rust bindings for cairo contracts
-
ecdna-lib
The ecDNA distribution for the evolutionary of extra-chromosomal DNA (ecDNA)
-
holochain_integrity_types
Holochain integrity types
-
prot_translate
Translate nucleotide sequence to protein
-
small-bwt
BWT construction in small space
-
nucleic-acid
Implementations of Suffix Array, Burrows-Wheeler Transform and FM-index
-
holochain_http_gateway
The Holochain HTTP Gateway for providing a way to bridge from the web2 world into Holochain
-
nucleobases
low-level brick crate for managing nucleobases as data in code
-
jean
Computational biology utility library for Rust featuring sequence alignment, genome annotation, and I/O of biological files
-
optimigation
tools for evolutionary computation, participate GA
-
nucleociph
encoding phrases into nucleotide characters, and vice versa
-
holochain_scaffolding_cli
CLI to easily generate and modify holochain apps
-
khat
A cat clone, nothing more nothing less
-
basebits
encoding DNA into u64 to allow for constant time hamming distance calculations
-
classeq-core
Core library for the classeq project
-
omics-molecule
Foundational representations of biological molecules in the Rust omics ecosystem
-
holochain_deepkey_dna
A compilation of the Deepkey DNA for use in Holochain
-
sdust
symmetric DUST algorithm, with optional CLI
-
rust-spoa
wraps the C++ SPOA library for generating DNA and protein consensus sequences
-
deepbiop-core
Deep Learning Preprocessing Library
-
kmers
k-mer manipulation
-
digest-rs
Rust bindings for the digest library
-
omics-coordinate
Foundational representations of coordinates in the Rust omics ecosystem
-
pingpong-rs
A Rust-based TUI ping utility for monitoring network connectivity to multiple hosts simultaneously
-
kmers-rs
k-mer manipulation
-
holochain_cli_sandbox
CLI to help create, run and interact with sandboxed Holochain conductor environments, for testing and development purposes
-
blend-rs
read Blender's .blend files
-
sequence_domain
A DNA/RNA sequence domain
-
rust-gc-count
GC and sequence utilities
-
multi-seq-align
Manipulate multiple sequence alignments (DNA/protein)
-
classeq-ports-lib
A base library to share elements between Classeq ports
-
protein_translation
translate &str or String of RNA sequence with nucleotide into a Vec<&str> of their appropriate protein names
-
classeq-watcher
watcher for the Classeq project
-
lrdf
Commandline tool to generate a dataframe from Oxford Nanopore FastQ
-
holochain_types
Holochain common types
-
jean_io
I/O library feature for jean
-
hc_portal_types
Definitions used by the Portal DNA Zomes
-
jean_cut
Codon usage tables feature for jean
-
genome
package used to generate DNA used for GAN generator
-
jean_macros
Macro library feature for jean
-
holochain_cli
hcbinary, a helpful CLI tool for working with Holochain -
hc_deepkey_sdk
SDK for the Deepkey DNA Zomes
-
unblend
A program to explode blend files into their many parts
-
ncrs
A lightweight Rust library for loading and storing nucleic acid sequences (DNA or RNA) and their annotations with minimum dependences
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