Science::Bioinformatics

FASTA format reader and writer

Coordinate-sorted index (CSI) format reader and writer

Bioinformatics I/O libraries

Tabix (TBI) format reader and writer

Sequence Alignment/Map (SAM) format reader and writer

BED (Browser Extensible Data) reader and writer

Shared utilities when working with noodles

Binary Alignment/Map (BAM) format reader and writer

Gene Transfer Format (GTF) reader and writer

Variant Call Format (VCF) reader and writer

Binary Call Format (BCF) reader and writer

FASTQ format reader and writer

Generic Feature Format (GFF) reader and writer

CRAM format reader and writer

noodles support utilities

An htsget client

A refget client

DNA and RNA sequence types and functions

Constructing and iterating packed DNA sequences using SIMD

A SIMD-accelerated library to compute random minimizers

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

Microbiology friendly bioinformatics Rust functions

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

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

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

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

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

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

Performance critical tools for genomic interval analysis.

fuzzyfold's nearest neighbor free energy evaluations.

High-performance FASTQ reader with mmap-first design. Supports plain, gzip, and BGZF inputs; optional multi-line parsing; and explicit paired-end reading.

Deterministic mitochondrial QC scoring for single-cell expression matrices.

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

A high efficiency binary format for sequencing data

A library for converting alevin-fry output to the AnnData format

fuzzyfold's secondary structure representations.

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

FastQC-compatible QC tool written in Rust

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

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

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

fuzzyfold's stochastic secondary structure simulations.

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

Parser for Gene Ontology Consortium GO-CAM files

FM-index library with slice view architecture for efficient text indexing and pattern matching

Nucleic acid secondary structure kinetics.

A type-safe Nightscout client for Rust, aiming to simplify the interactions with the confusing Nightscout API.

A fast and memory-efficient FASTX PCR deduplication tool

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. The goal is drop-in compatibility with bwa-mem pipelines while supporting long reads efficiently.

A command-line tool for interacting with BINSEQ file formats.