| --- |
| license: gpl-3.0 |
| tags: |
| - umi |
| - molecular-barcodes |
| - sequencing |
| - immunogenomics |
| pretty_name: UMI benchmark data for migec |
| --- |
| |
| # umi_data |
| |
| Fixtures and derived results for [**migec**](https://github.com/antigenomics/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. |
|
|
| ```bash |
| migec refine ci/SRR1763769_umi0.5pct.fq.gz -o ref/ |
| migec assemble ref/CTRL.fq.gz -o cons/ |
| ``` |
|
|
