bio

Rust crates for working with genomic data and building bioinformatics tools.

Crates

• biocore: Core types and parsers for biological data: DNA/RNA sequences, amino acids, genomic locations, VCF/BCF files, FASTA readers, and mutation representations. Built on noodles for format support. Note that genomic coordinates are 0-indexed internally (because it makes writing software easier).

• liftover: Genome coordinate conversion between assemblies (GRCh37 ↔ GRCh38, etc.). Parses UCSC chain files and provides both naive and indexed lookups. Handles strand orientation.

• puv: Rust-Python interop using PEP 723 inline script metadata. Executes typed Python functions from Rust with automatic JSON serialization and uv-managed dependencies.

• primeedit: Prime editing guide RNA design. Generates pegRNA designs from sequence edits, validates PAM sites, computes RTT templates, and checks for seed/PAM disruption. Includes silent mutation insertion for MMR evasion.

• pgs_catalog: Client for the PGS Catalog (Polygenic Score Catalog). Loads scoring files and harmonized variants across genome builds. Handles the catalog's complex metadata and provides simplified representations for downstream analysis.

• gwas_catalog: Client for the GWAS Catalog. Fetches and deserializes association data, study metadata, and ancestry information.

• pan_ukbb: Loader for Pan-UK Biobank summary statistics.

• genomes1000: Parser and loader for 1000 Genomes Project high-coverage VCF data. Handles multi-allelic splitting, normalization, and querying with tabix indexes. Includes pedigree information. Note: I handwrote the parser for fun, but you probably wants something that skips most of the metadata.

• ids: Newtypes for identifiers: RsId, PgsId, PubmedId. Provides parsing and validation.

• ensembl / hail: Resource helpers for Ensembl and Hail reference genomes with embedded contig metadata for GRCh37/GRCh38.

• utile: Useful utilities.

Requirements

• Requires nightly (see rust-toolchain.toml).