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README.md

@@ -34,6 +34,44 @@ Each `.bw` file contains:
 - Header string (variable length)
 - Packed 2-bit bases
 
+## Tools
+
+### `bw` -- DNA ripgrep
+
+Install the [Bitwise](https://github.com/forkjoin-ai/bitwise) CLI to search these datasets:
+
+```bash
+cargo install --path .  # from the bitwise repo
+
+# Search for a pattern across a gene
+bw grep GGTGGCGTAGGC cancer-genes/fasta/KRAS.fasta
+
+# Count mutations between reference and tumor
+bw count reference.fasta tumor.fasta
+
+# Compression stats
+bw stats cancer-genes/fasta/BRCA1.fasta
+```
+
+Search speed: **90 million bases per second** on a single CPU core.
+
+### Aeon FlowFrame Protocol
+
+These datasets stream natively as [Aeon FlowFrames](https://github.com/forkjoin-ai/aeon-flux):
+
+```
+stream_id = chromosome (1-25)
+sequence  = genomic position
+flags     = FORK | FOLD | VENT (structure type)
+payload   = 2-bit packed bases
+```
+
+Wire = storage = memory. No serialization boundary.
+
+### helix.repair
+
+Search these datasets live at **[helix.repair](https://helix.repair)** -- a DNA topology search engine powered by Bitwise encoding and 402 Lean theorems.
+
 ## Datasets
 
 ### cancer-genes/
@@ -158,9 +196,7 @@ Code: MPL-2.0
 | chrY | 57,227,415 | 14 MB |
 | chrM | 16,569 | 4.1 KB |
 
-Available on HuggingFace: `huggingface-cli download forkjoin-ai/bitwise-genomes hg38/`
-
-Or reproduce locally:
+**Too large for GitHub.** Reproduce locally:
 
 ```bash
 # Download and convert (requires ~4GB disk)