umi_data

Fixtures and derived results for migec — UMI barcode extraction, correction and consensus assembly.

This dataset holds sequences and metadata, and nothing else:

• ci/ - small fixtures, cut from public data, that the test suite and the documentation examples run against.
• SOURCES.md - where every file came from and the exact command that regenerates it.

Permitted file types: .txt, .md, .tsv.gz, .json, .fastq.gz, .fa.gz, .sam, .bam. No reports, figures, logs or pipeline output. A derived results table is output, not data, even when it is a TSV - those live in the code repository next to the script that made them.

What is deliberately not here

• Raw reads that are one command away. SRR1763769 is 248 MB on ENA and a curl recovers it exactly; SOURCES.md carries the command instead of the bytes.
• Simulated corpora. Regenerable from a seed, and the seed is in SOURCES.md.
• Anything under access control. Nothing in this dataset came off a private cluster.

ci/SRR1763769_umi0.5pct.fq.gz

2.12 M reads of an HIV-1 Primer ID library, checked out on a 9 nt Primer ID, then cut down to all of the reads of 0.5% of the barcodes — 9,824 reads over 623 barcodes.

Never: Not a 0.5% sample of the reads. At 16 reads per molecule, sampling reads gives molecules seen once each: the MIG size distribution is destroyed and every consensus is a single read, so the fixture silently stops testing the thing it was built for. The barcodes are selected by hashing (splitmix64 of the packed barcode, kept when hash % 10000 < 50), which is unbiased, nested — a smaller fixture is a subset of a larger one — and reproducible from the definition in include/migec/subsample.hpp.

The fixture keeps 15.77 reads per barcode against the full library's 16.05.

migec refine  ci/SRR1763769_umi0.5pct.fq.gz -o ref/
migec assemble ref/CTRL.fq.gz -o cons/