Prebuilt hg38 reference indexes v1 (reference data only)

Prebuilt hg38 reference indexes — v1

Reference data only: this does not replace the latest OncoTracer software release.
The bundle contains the public UCSC hg38 genome from AWS iGenomes, plus BWA and minimap2 indexes. It contains no patient reads, sample information, tumor predictions, or model weights.

Install the command

The existing v2.0.0 executable does not have reference install. Use this tested source revision in a new software directory:

git clone --branch hg38-reference-v1 https://github.com/cfarkas/oncotracer.git oncotracer-src
python3 -m venv oncotracer-env
oncotracer-env/bin/python -m pip install -e ./oncotracer-src
source oncotracer-env/bin/activate

Keep both folders. Linux and Python 3.10–3.13 are required. The reference tag fixes source revision 6419b2aefba915457ff98da660ffbc4d7fc8f414; Git's detached-HEAD notice is expected for a tagged checkout.

Download and install the indexes

Choose a new, reusable reference parent, replacing /absolute/path/shared-reference below:

oncotracer reference install \
  --manifest https://github.com/cfarkas/oncotracer/releases/download/hg38-reference-v1/hg38-reference.json \
  --sha256 1c704b1522fe37c13bf4272858792d03e827bc476fdb6712fa7f760f3c944632 \
  --lpwgs-root /absolute/path/shared-reference \
  --mode ont --dry-run

--manifest is the inventory URL; --sha256 verifies it; --lpwgs-root is where reusable references will live. --mode ont installs the ONT index, illumina selects BWA, and both installs both. --dry-run previews space and destination. Remove it to download and install. You do not need to download individual .part files manually.

Set lpwgs_root: /absolute/path/shared-reference in the project YAML. The installed directory is shared-reference/references/samurai_hg38/. Existing references are never overwritten. An interrupted import can be restarted, but partial downloads are not resumed.

Allow approximately 8.0 GiB for Illumina, 9.7 GiB for ONT, or 14.8 GiB for both, plus 1 GiB of free headroom. The importer verifies each chunk and complete file without loading or building an index. The complete public HTTPS download/import passed under a 1-GiB address-space limit with 42,940 KiB peak RSS (about 42 MiB), no swap and zero index builds. This is not an alignment-memory requirement: analysis needs more RAM. Use oncotracer system --path /absolute/path/project for planning guidance.

Tool compatibility

These indexes were validated with Linux x86-64 Bioconda BWA 0.7.19=h577a1d6_1 and minimap2 2.30=h577a1d6_0. Analysis verifies exact executable hashes and stable package metadata; a different build is rejected rather than silently rebuilding the shared reference. Other architectures/builds need a separately validated bundle.

Fresh installations of both tools accepted the public download through OncoTracer's normal reference checks and correctly mapped synthetic short/long reads without rebuilding indexes. This checks index usability, not a complete CNA workflow or tumor-classifier accuracy.

The manifest pins all genome, index, and chunk hashes. Usability changes and software test status are tracked separately. This is research software, not a standalone diagnostic system.