bio-blat

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Runs local BLAT searches for DNA sequence alignment against hg38 or CHM13 using local .2bit references. Use when a user wants to align a DNA sequence without relying on UCSC API access.

1installs

Sourcedakesan/cc-dnawork-plugin

Added on2026-02-21

NPX Install

npx skill4agent add dakesan/cc-dnawork-plugin bio-blat

SKILL.md Content

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BLAT API Searching

Quick start

Run BLAT locally via the Python CLI script. The script manages reference downloads.

Utility script

Install dependencies:

bash

uv pip install typer

Run BLAT with a FASTA file:

bash

python scripts/run_blat_local.py run --reference hg38 --fasta path/to/query.fasta

Run BLAT with a raw sequence:

bash

python scripts/run_blat_local.py run --reference CHM13 --sequence ACTG...

Save JSON output to a file:

bash

python scripts/run_blat_local.py run --reference hg38 --sequence ACTG... --output blat.json

When to read references

Local BLAT setup and references: See
```
references/local_blat.md
```

Workflow (local-only)

Confirm the reference assembly (
```
hg38
```
or
```
CHM13
```
).
Ensure the 2bit reference exists in
```
~/.local/share/blat
```
.
Use the CLI script to run BLAT and get a PSL output.
If FASTA has multiple sequences, split into one sequence per file.

bio-blat

NPX Install

Tags

SKILL.md Content

BLAT API Searching

Quick start

Utility script

When to read references

Workflow (local-only)