biocommons.seqrepo

What it is and what it does

SeqRepo is a Python package for managing local collections of biological sequences with efficient, non-redundant storage. It solves the problem of maintaining multiple reference genomes and sequence databases locally by providing a compressed, indexed repository that supports fast random access to sequence regions. Sequences are stored using Block GZipped Format (BGZF) compression and identified via multiple namespace conventions (RefSeq, Ensembl, hash digests), allowing callers to refer to sequences using familiar accessions like NM_000551.3 or GRCh38:1.

The package is designed for bioinformatics workflows where reproducible access to versioned sequence snapshots is critical. It supports timestamped, read-only snapshots that can be mirrored from public sources or maintained locally via CLI or API. Dependencies include bioutils, pysam (for BGZF access), requests, yoyo-migrations, and utility libraries like coloredlogs and tqdm. The repository structure uses SHA-512 truncation for deduplication and SQLite for alias mapping, making it suitable for chromosome-scale sequences and multi-snapshot deployments.

Use it for:

• Build a local mirror of RefSeq and Ensembl genomes for reproducible variant annotation pipelines
• Resolve sequence identifiers from multiple naming conventions to a canonical sequence in a single query
• Retrieve arbitrary slices of large reference genomes without loading entire sequences into memory
• Maintain versioned snapshots of reference data for compliance or reproducibility in clinical genomics workflows
• Serve sequences via REST API using seqrepo-rest-service for distributed bioinformatics applications

Worth the install?

AI-flagged interpretation of the facts on this page — verify before relying

SeqRepo stores and retrieves biological sequences in a non-redundant, compressed, indexed repository, supporting fast slicing and multiple sequence identifiers including RefSeq accessions, Ensembl IDs, and hash-based aliases.

Yes, if you need local, versioned biological sequence storage for bioinformatics pipelines. The package is well-maintained (active commits, no vulnerabilities), has low install friction, and solves a real problem in genomics workflows. Caveat: last release was 513 days ago and development is aging; verify that the snapshot versions and reference data you need are current before committing to production use.

Install

biocommons-seqrepo on PyPI

pip install biocommons-seqrepo

uv add biocommons-seqrepo

poetry add biocommons-seqrepo

Installing biocommons.seqrepo

Before you install

Low install friction with a pure-Python wheel and eight runtime dependencies. Maintenance status is aging—last release was 513 days ago—but the repository remains active with recent commits and no archived status.

License in practice

Licensed under Apache License 2.0 (permissive), allowing commercial and private use with minimal restrictions.

Quickstart

pip install biocommons.seqrepo

from biocommons.seqrepo import SeqRepo
sr = SeqRepo("/usr/local/share/seqrepo/latest")
sequence_slice = sr["NC_000001.11"][780000:780020]

Requires rsync binary for CLI-based snapshot acquisition; writing sequences requires bgzip from htslib (Ubuntu: install tabix package). Mac users must install rsync from HomeBrew as openrsync lacks required functions.

Verify before relying

• Performance characteristics for very large sequence queries or concurrent access patterns
• Compatibility with non-Ubuntu/non-macOS systems beyond stated development platforms
• Scalability limits for repository size or number of snapshots

Package facts

Evidence: biocommons.seqrepo-0.6.11-py3-none-any.whl

Tags

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