Science::Bioinformatics

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.

Coordinate-sorted index (CSI) format reader and writer

FASTA format reader and writer

Bioinformatics I/O libraries

Tabix (TBI) format reader and writer

Binary Alignment/Map (BAM) format reader and writer

Sequence Alignment/Map (SAM) format reader and writer

Gene Transfer Format (GTF) reader and writer

BED (Browser Extensible Data) reader and writer

Constructing and iterating packed DNA sequences using SIMD

Variant Call Format (VCF) reader and writer

Generic Feature Format (GFF) reader and writer

Binary Call Format (BCF) reader and writer

A SIMD-accelerated library to compute random minimizers

CRAM format reader and writer

Shared utilities when working with noodles

noodles support utilities

FASTQ format reader and writer

Microbiology friendly bioinformatics Rust functions

A SIMD-accelerated library to compute hashes of DNA sequences

DNA and RNA sequence types and functions

An htsget client

A refget client

fuzzyfold's secondary structure representations.

A viewer of multiple sequence alignments, with a text user interface

A high efficiency binary format for sequencing data

Gene-field extraction and deterministic signal transforms for spatial transcriptomics.

SIMD-accelerated library for FASTA/FASTQ parsing and bitpacking

Performance critical tools for genomic interval analysis.

fuzzyfold's stochastic secondary structure simulations.

fuzzyfold's nearest neighbor free energy evaluations.

Deterministic single-cell input reader stack for MTX/H5AD/BD Rhapsody in Kira tools.

High-performance FASTQ reader and writer with mmap-first design. Supports plain, gzip, and BGZF inputs/outputs; optional multi-line parsing; explicit paired-end reading; sync and async APIs; optional `noodles-bgzf` interop.

A library for efficient nucleotide sequence manipulation using 2-bit and 4-bit encodings

Fast gradient calculation of the Felsenstein algorithm with respect to the rate matrix

Compatibility alias crate for the canonical bijux-atlas-runtime library surface

View, edit, and explore multiple sequence alignments in your terminal

Deterministic mitochondrial QC scoring for single-cell expression matrices.

A fast and memory-efficient FASTX PCR deduplication tool

A library for OME-Zarr (previously OME-NGFF) metadata

Deterministic spatial transcriptomics IO primitives for Kira.

Deterministic spatial math and contour primitives for transcriptomics 3D pipelines.

Ultra high-throughput processing of 10x-flex single-cell sequencing data

Low-level, streaming mmCIF/BinaryCIF parser focused on protein coordinates.

Shared deterministic binary cache reader/writer for Kira single-cell pipelines (kira-organelle.bin and expr.bin).

Performance critical tools for genomic interval analysis. This is the CLI

Deterministic 3D mesh, contour, and export primitives for spatial omics fields.

Nucleic acid secondary structure kinetics.

Runtime-independent Atlas core primitives and invariants

Deterministic, explainable secretion-state QC for single-cell expression data.