# BCL Demultiplexing Benchmark

This is the raw Illumina run-folder barcode demultiplexing evidence track.

Current status: DotMatch supports a first lane-1 classic per-cycle BCL milestone. CBCL/NovaSeq-style input and broader multi-lane BCL operation are still gated as future work. Broader comparisons need real run folders and zero-mismatch validation against BCL Convert or bcl2fastq where available.

The public `public_10x_tiny_bcl` row uses the 10x Genomics Cell Ranger `tiny-bcl` mkfastq demo run folder. The bundled fetch script downloads the 10x sample sheet, the public run-folder archive, and the official Chromium i7 index CSV used to normalize the legacy `SI-P03-C9` index-set alias into concrete index sequences.

Rows with exit code `127` are environment records for missing competitors, not runtime comparisons. They are kept in the raw table so the report is explicit about what was unavailable on this machine.

## Figures

![Throughput](../../../benchmarks/figures/bcl_demux_throughput.svg)

![Peak memory](../../../benchmarks/figures/bcl_demux_peak_memory.svg)

![Assigned reads](../../../benchmarks/figures/bcl_demux_assigned_reads.svg)

## Raw Rows

| tool | workflow | format | clusters | cycles | samples | threads | gzip | seconds | clusters/sec | peak RSS KB | output MB | assigned | undetermined | filtered | validation | mode | content hash | exit | logs |
| --- | --- | --- | ---: | ---: | ---: | ---: | ---: | ---: | ---: | ---: | ---: | ---: | ---: | ---: | ---: | --- | --- | ---: | --- |
| dotmatch_bcl_demux | public_10x_tiny_bcl | classic_bcl | 2136539 | 132 | 1 | 1 | 1 | 10.029591 | 213023.5 | 297184 | 200.06 | 2079501 | 57038 | 0 |  |  | 2f4c38035535 | 0 | ../../../benchmarks/work/bcl_demux/logs/dotmatch_bcl_demux.stderr.log |
| bcl-convert | public_10x_tiny_bcl | classic_bcl_or_cbcl | 2136539 | 132 | 1 |  |  | 0.000000 | 0.0 | 0 |  |  |  |  |  |  |  | 127 |  |
| bcl2fastq | public_10x_tiny_bcl | classic_bcl_or_cbcl | 2136539 | 132 | 1 |  |  | 0.000000 | 0.0 | 0 |  |  |  |  |  |  |  | 127 |  |
| cuda-demux | public_10x_tiny_bcl | classic_bcl_or_cbcl | 2136539 | 132 | 1 |  |  | 0.000000 | 0.0 | 0 |  |  |  |  |  |  |  | 127 |  |

## Scope

Run `make bcl-tiny-public-gate` to verify the narrow public 10x tiny-BCL classic per-cycle milestone. This gate checks the committed DotMatch row, output hashes, count totals, and bcl2fastq count-total validation when bcl2fastq is available; an explicit `not_installed` environment row keeps the boundary visible without turning it into a false comparison.

Broader raw-BCL evaluation needs real classic-BCL and CBCL run-folder rows, a successful DotMatch CBCL row, competitor rows for BCL Convert/bcl2fastq/CUDA-Demux where installable, distinct repeated timing, and `dotmatch bcl-validate` zero-mismatch evidence.

Use `make bcl-comparison-gate` to check those rows when they are available.