# rust-bio/rust-bio

This library provides implementations of many algorithms and data structures that are useful for bioinformatics. All provided implementations are rigorously tested via continuous integration.

Repository: https://github.com/rust-bio/rust-bio
Canonical: https://ross.abutalabs.com/products/rust-bio
Homepage: https://rust-bio.github.io
Language: Rust
License: MIT
License Family: permissive
Last push: 2026-07-27T04:53:31+00:00

## Health v2 (maintenance only)
Score: 90/100 (v2, computed 2026-09-02T17:46:02.011165+00:00)
- activity 94, release rhythm 78, longevity 100
- inputs: {"age_days": 4238, "days_push": 37, "days_rel": 65, "gap_med": 76, "n_releases_24m": 8}
- flags: none
- formula: round(0.45*activity + 0.35*rhythm + 0.20*longevity); archived -> min(score, 10)

## Adoption (not part of the score)
Stars 1837, forks 220 (observed 2026-08-28T04:05:42.729386+00:00)

## What it is
Rust-Bio is a Rust library providing implementations of algorithms and data structures useful for bioinformatics, such as sequence alignment, pattern matching, and quality score handling. All implementations are rigorously tested via continuous integration and published on crates.io as the `bio` crate.

## Use cases
- implement sequence alignment algorithms in Rust
- parse and process FASTA and FASTQ files
- build bioinformatics pipelines in Rust
- perform pattern matching on genomic sequences
- compute pairwise and multiple sequence alignments
- work with BWT and suffix arrays for text indexing
- handle paired-end reads and quality scores

## When to choose
- you are writing bioinformatics tools in Rust and need well-tested algorithm implementations
- you want a fast, memory-safe alternative to BioPython or BioPerl
- you need core bioinformatics data structures like BWT, FM-index, or alignment algorithms
- you value CI-tested, MIT-licensed library code with an active community

## When to avoid
- you need a full-featured GUI or command-line bioinformatics application out of the box
- your project is in Python, Java, or another language without Rust integration
- you need highly specialized algorithms not covered by the library's modules
- you require commercial support or extensive documentation beyond the API docs

## Facets
- artifact type: library
- maturity: stable
- function: parser, data-science, developer-tools
- domain: bioinformatics, data-science
- platform: rust, cross-platform
- tags: bioinformatics, rust, sequence-analysis, algorithms, data-structures, genomics

## Member repositories
- rust-bio/rust-bio (main) score 90

## Provenance
- Observed fields: from GitHub, fetched 2026-08-28T04:05:42.729386+00:00.
- Health v2: computed from the inputs above; adoption is never an input.
- Inferred fields (summary, facets, guidance): AI-extracted, prompt v1, taxonomy v1, on 2026-08-30T03:18:26.886204+00:00, confidence not recorded.
  - readme: https://github.com/rust-bio/rust-bio (fetched 2026-08-28T04:05:42.729386+00:00, sha 67d8e953f66d)
  - homepage: https://rust-bio.github.io (fetched 2026-08-29T10:57:29.278054+00:00, sha 50f71301eeb9)
- Data as of 2026-08-30T08:39:29.467469+00:00.