README.md

metadata

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'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.