| --- |
| 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. |
|
|
