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license: cc-by-4.0
tags:
- single-cell
- genomics
- benchmark
- seqforge
pretty_name: seqforge validation benchmark
---
# seqforge validation benchmark
Byte-light **fingerprint packages** for [`seqforge`](https://github.com/liuhlab/seqforge)'s validation
benchmark. Each `packages/<accession>.fingerprint.tar.gz` is a head-slice of a real public dataset's
FASTQs (the first ~2000 reads per file) plus a pin carrying the whole-file identity — enough for
seqforge to reproduce the same `manifest.yaml`, hash and all, **without the original FASTQs**. This is
the growing validation set the compiler is developed against; a true held-out test set is separate.
## What's here (and what's not)
- **Reads:** head slices only — never a whole FASTQ. Enough to fingerprint the chemistry, far too few
to reconstruct the biology.
- **Prose:** extracted **text only** (`info/text/`). The raw papers and their figures are **not**
redistributed here (copyright); the packages are built with `seqforge preflight --redistributable`
(or repacked with `seqforge strip-fingerprint`), which is why they are usable for harvest yet carry
nothing that may not be shared.
## How it is used
seqforge's eval harness pulls a package by accession (anonymous, pooch-cached — no token) and runs the
real compiler over the slice, grading the resolved library against a pre-registered `expected.yaml`
committed in the repo. Sample-level facts are graded from the archive's own BioSample/SRA records, also
committed in the repo. See `evals/benchmark/` in the seqforge repository.
## Datasets
All *C. elegans* (taxid 6239), chosen to span technology × prep × layout × known regressions at
moderate sample size:
| accession | chemistry | notes |
|---|---|---|
| PRJNA1027859 | 10x 3' v3/v3.1 | single-nucleus neurons (the pilot demo dataset) |
| GSE274290 | BD Rhapsody WTA | the only BD-original dataset; germline |
| GSE234962 | 10x 3' v3 | motor neurons |
| GSE256266 | 10x 3' v3/v3.1 | glia across sexes; irregular filename layout |
| PRJNA658829 | 10x 3' v3 | whole-organism; equal-length read layout |
| PRJNA1195922 | 10x 3' v3/v3.1 | male single-nucleus neurons |
| GSE126954 | 10x 3' v2 | embryogenesis atlas |
The set grows as more datasets are curated.
|