liulab-genome
Reference genomes on disk, ready to query. Name an assembly and it is fetched, prepared
(.fai, .2bit, chrom.sizes) and answering sequence queries — plus GTF annotations
registered against it and STAR/chromap indexes built from it.
Import name: genome.
from genome import Genome
sacCer3 = Genome("sacCer3")
sacCer3.fetch_sequence("chrIV:0-10") # DNA('ACACCACACC') — 0-based, half-open
Docs: https://liuhlab.github.io/liulab-genome/
Development
This project uses pixi with conda-forge + bioconda channels. Native
deps (samtools, bedtools) and Python tooling are all managed by pixi.
pixi install # solve & install the default env (resolves from pixi.lock if present)
pixi shell # activate the env
pixi run check # lint + fmt-check + typecheck + test, run concurrently (the gate)
pixi run -e aligners test-aligner # the other lane: the tests that build a real STAR/chromap index
See AGENTS.md (CLAUDE.md symlinks to it) for the full contributor/agent working agreement.
License
MIT — see LICENSE.
1 maintainer
Metadata
1 maintainer
Release files for liulab-genome 2026.8.0
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