SOURCES — antigenomics/migec
Every dataset this repo ships, consumes or benchmarks against, where it came from, and how to regenerate it.
Experimental = measured/sequenced. Derived = computed by us from something else. The two are never conflated in a table row.
Shipped in this repo
| Artifact | Origin | Provenance | Regenerate |
|---|---|---|---|
tests/synthetic/_sim.py output |
none — generated | derived | SimConfig(seed=...); every truth file is a pure function of the seed |
tests/cpp/doctest.h |
doctest 2.4.11, MIT | vendored | copy from upstream release |
Nothing else is committed. Test corpora live on HuggingFace (below) rather than in git.
Benchmark data
Nothing here has been fetched yet — this table is the plan of record, and rows gain a "fetched" date as they land.
MIGEC (Shugay et al., Nat Methods 2014, doi:10.1038/nmeth.2960)
| Item | Value |
|---|---|
| Public spike-ins | BioProject PRJNA239303, runs SRR1200517–SRR1200520, AMPLICON paired |
| Ground truth | Supplementary Table 1a: 12 control clonotypes (5 TRA, 5 TRB, 2 IGH) with expected frequencies |
| Truth source | 41592_2014_BFnmeth2960_MOESM376_ESM.pdf, extractable with pdftotext -layout |
| Provenance | experimental |
| Chemistry | MiSeq 2×150; SMART adapter GTGGTATCAACGCAGAG |
| Item | Value |
|---|---|
| Experiment 1 (internal) | /projects/cdr3_ngs/2012/12_alvaro_ab_bcr_nnn/ (IGH) and /projects/cdr3_ngs/2012/08_alvaro_nnnb/ (TCR) on aldan3 |
| Staged copies | /projects/tcr_bcr_rnaseq/data_migec_exp1/{IGH_P41,TCR_Project25}_R{1,2}.fastq.gz |
| Access | aldan3 ls, aldan3 pull (see ~/vcs/code/aldan3-client) |
| Provenance | experimental, unpublished |
Never: Experiment 1 raw reads must not leave the cluster. Only derived summaries (histograms, error-rate tables, consensus statistics) may be published or uploaded to HuggingFace.
Never: scratch/spikein/S1_R2_2M.fq on aldan3 is corrupt past record 1,742,617. Do not use it.
MAGERI (Shugay et al., PLoS Comput Biol 2017, doi:10.1371/journal.pcbi.1005480, PMID 28475621)
| Item | Value |
|---|---|
| Error-model datasets | SRA PRJNA352143 — UMI-tagged sequencing of a known template with 9 polymerases |
| Duplex sequencing | SRA SRR1799908; primer patterns NNNNNNNNNNNNtgact / agtcaNNNNNNNNNNNN |
| HIV protease amplicons | SRA SRP052322; patterns NNNNNNNNNcagtttaacttttgggccatccattcc / ctatcggctcctgnnnn |
| Companion repo | https://github.com/mikessh/mageri-paper (error model PDFs, analysis scripts) |
| Provenance | experimental |
The patterns above are quoted verbatim from the paper's Methods and are directly reusable as
checkout test cases.
Reference values worth keeping (MAGERI Methods, for comparison rather than reimplementation):
UMIs below Phred 20 discarded; MIG pairs differing by 1 or 2 substitutions with size ratios above
20× and 400× treated as error children; MIG size threshold at the square root of the distribution
peak; consensus core 30 bases with ±5 offset; CQS = (40/3)·(4f − 1); per-substitution error
rates fitted as Beta, counts as Beta-Binomial, Q = −10 log10 P, capped at 100.
10x Genomics
| Item | Value |
|---|---|
| Datasets | four "Connect-generated GEX+VDJ" sets: human PBMC, mouse PBMC, human melanoma, mouse splenocytes (Cell Ranger 6.0.1) |
| Whitelists | barcode whitelists shipped with Cell Ranger (10XGenomics/cellranger) |
| Reference calls | the published filtered_feature_bc_matrix — used as a comparator, not re-run |
| Provenance | experimental (10x), reference calls derived |
X1 (read-start dispersion) used pbmc_1k_v3, Cell Ranger 3.0.0, GRCh38-3.0.0:
| Item | Value |
|---|---|
| BAM | https://cf.10xgenomics.com/samples/cell-exp/3.0.0/pbmc_1k_v3/pbmc_1k_v3_possorted_genome_bam.bam (4.79 GB) + .bai (4.6 MB) |
| Fetch | not fetched — the server serves HTTP range requests (verified 206, 2026-08-13), so pysam.AlignmentFile(url) reads only the regions asked for |
| Regions | 11:65497688-65508073 (MALAT1), 7:5527151-5530601 (ACTB), 15:44711477-44718877 (B2M) — chosen for expression, since an unexpressed locus has no UMI with more than one read |
| Contig names | plain 1, 2, … X — not chr1. Cell Ranger's GRCh38-3.0.0 reference is Ensembl-styled |
| Regenerate | python scripts/read_start_dispersion.py --bam <url> --region … |
| Provenance | experimental (10x); the dispersion statistics are derived |
HIV-1 Primer ID — the X2 quality-floor control
| Item | Value |
|---|---|
| Run | SRR1763769, 2,122,456 read pairs, study PRJNA272736 |
| Fetch | curl -O ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR176/009/SRR1763769/SRR1763769_2.fastq.gz (248 MB; R1 is not needed — the Primer ID is on the cDNA primer in R2) |
| Layout | 9 nt Primer ID, then CAGTTTAACTTTTGGGCCAT; recovered from the data by per-cycle entropy, not from the protocol |
| Paper | Zhou, Jones, Mieczkowski & Swanstrom, J Virol 89(16):8540–8555, 2015, doi:10.1128/JVI.00522-15 — reports a residual error rate of ~1 in 10,000 |
| Regenerate | python scripts/quality_floor.py --reads SRR1763769_2.fastq.gz --out x2/ --window 180 (X2, the quality floor) and python scripts/permutation_nulls.py --reads SRR1763769_2.fastq.gz --out x3/ --cycles 32 --window 180 (X3, the three permutation nulls) |
| Provenance | experimental (ENA); the floor and its interval are derived |
| Note: | ENA's metadata gives every run in the study the same title, so it does not identify which runs are controls. This is HIV plasma — a quasispecies — so the estimator restricts to monomorphic positions rather than assuming clonality. The library is also 49.6% occupied on its 9 nt barcode, which checkout flags as saturated; the measured floor is an upper bound. |
Calib (github.com/vpc-ccg/calib)
| Item | Value |
|---|---|
| Use | comparator for UMI grouping accuracy — it clusters on barcode and sequence, we (today) on barcode alone |
| Get it | git clone https://github.com/vpc-ccg/calib && cd calib && make → calib, calib_cons |
| Run | calib -f R1.fq -r R2.fq -l <barcode_len> -o prefix → prefix.cluster |
.cluster format |
9 TSV columns: cluster_id, node_id, read_id, f_name, f_seq, f_qual, r_name, r_seq, r_qual (verified against the upstream README, 2026-08-13) |
| Truth used here | our simulator, tests/synthetic/_sim.py, which writes truth_reads.tsv (read_id, molecule_id). Calib's own simulator emits no read→molecule map |
| Compared by | scripts/compare_calib.py — adjusted Rand index, plus split and merge fractions separately |
| Storage | Never: do not store simulated reads — record the exact command and seed here instead |
| Provenance | derived (simulated) |
HuggingFace — isalgo/umi_data
Does not exist yet. When created: a git + git-lfs mirror at ~/hf/umi_data, written by
committing and pushing in the mirror, one commit per change set. Never through the HTTP API —
that writes remotely only, leaves the mirror silently stale, and lands one commit per call.
Planned layout:
umi_data/
ci/ small slices for CI, subsampled by WHOLE UMIs (all reads of N UMIs)
truth/ ground-truth tables (spike-in clonotypes, simulated molecule tables)
whitelists/ barcode whitelists + a README recording their upstream and license
SOURCES.md
Never: Not in this dataset: aldan3 Experiment 1 raw reads, and anything regenerable by a one-line command (record the command here instead of storing gigabytes in LFS).
What this HuggingFace dataset contains
Appended when isalgo/umi_data was first populated (2026-08-13). The sections above describe every
dataset migec uses; this section says which of them are shipped here and how each file was made.
ci/SRR1763769_umi0.5pct.fq.gz
| Item | Value |
|---|---|
| Origin | derived from SRR1763769 (ENA, PRJNA272736) — see the section above for the fetch command |
| Made by | migec suggest → migec checkout → migec subsample --keep 0.5 |
| Regenerate | migec suggest SRR1763769_2.fastq.gz gives NNNNNNNNNcagtttaacttttgggccatcca; migec checkout SRR1763769_2.fastq.gz -b barcodes.txt -o co/; migec subsample co/CTRL.fq.gz -o SRR1763769_umi0.5pct.fq.gz --keep 0.5 |
| Selection | splitmix64(packed barcode) % 10000 < 50 — deterministic, unbiased, nested |
| Provenance | experimental (ENA), subset by whole barcodes |
| Note: | 9,824 reads over 623 barcodes, 15.77 reads/barcode against the full library's 16.05 |
Never: Not shipped here
- aldan3 Experiment 1 raw reads. They do not leave the cluster; only derived summaries may.
- Britanova et al aging (bulk TCR, shallow). On aldan3, not yet pulled.
- Raw ENA runs. One
curlaway, so the command is shipped and the bytes are not. - Simulated corpora. Regenerable from the seed recorded above.
ci/sc5p_v2_hs_PBMC_1k_t_cells1pct.fq.gz
| Item | Value |
|---|---|
| Origin | 10x Genomics sc5p_v2_hs_PBMC_1k VDJ-T library (public), checked out and cut to 1% of CELLS |
| Made by | migec checkout R1 R2 -b bc.txt -o co/ --max-offset 0 with pattern XXXXXXXXXXXXXXXXNNNNNNNNNN, then migec subsample co/PBMC_R2.fq.gz --keep 1 |
| Contents | 18,036 reads over 2,636 molecules in 1,014 cell barcodes, 6.84 reads/molecule |
| Selection | whole cells, by splitmix64(packed cell barcode) % 10000 < 100 — a cell keeps every molecule in it |
| Why R2 | the barcode read (R1) is 26 nt of cell barcode and UMI and nothing else; the cDNA is all on R2, and both mates carry the tags |
| Provenance | experimental (10x), subset by whole cells |