Borzoi Tools

Configuration File: remote_tools/borzoi_tools.json Tool Type: Remote Tools Count: 2

This page contains all tools defined in the borzoi_tools.json configuration file.

Available Tools

run_borzoi_predict (Type: RemoteTool)

Predict multi-omic coverage (~7,611 human tracks, RNA-seq-dominant, plus CAGE/ATAC/DNase/ChIP) di…

run_borzoi_predict tool specification

Tool Information:

  • Name: run_borzoi_predict

  • Type: RemoteTool

  • Description: Predict multi-omic coverage (~7,611 human tracks, RNA-seq-dominant, plus CAGE/ATAC/DNase/ChIP) directly from a DNA sequence using Borzoi (Linder 2025), the successor to Enformer. The sequence is center-cropped / N-padded to 524,288 bp. Returns the central-bin value for requested tracks, or the top-signal tracks.

Parameters:

  • sequence (string) (required) DNA sequence (A/C/G/T/N). Cropped/padded to 524,288 bp around its center.

  • track_indices (array) (optional) Track indices to report (optional). If omitted, the top-signal tracks are returned.

  • top_n (integer) (optional) When track_indices is omitted, how many top tracks to return (default 20).

Example Usage:

query = {
    "name": "run_borzoi_predict",
    "arguments": {
        "sequence": "example_value"
    }
}
result = tu.run(query)

run_borzoi_variant_effect (Type: RemoteTool)

Score a variant with Borzoi: predicts coverage for the reference and alternate sequences (each 52…

run_borzoi_variant_effect tool specification

Tool Information:

  • Name: run_borzoi_variant_effect

  • Type: RemoteTool

  • Description: Score a variant with Borzoi: predicts coverage for the reference and alternate sequences (each 524,288 bp, variant at center) and returns the central-bin delta (alt - ref) per track — the canonical Borzoi expression/coverage variant-effect score, well suited to RNA-seq and splicing-proximal variants.

Parameters:

  • ref_sequence (string) (required) Reference DNA sequence centered on the variant (cropped/padded to 524,288 bp).

  • alt_sequence (string) (required) Alternate DNA sequence (same length/centering as ref).

  • track_indices (array) (optional) Track indices to report (optional; default = top |delta| tracks).

  • top_n (integer) (optional) When track_indices omitted, number of top |delta| tracks to return (default 20).

Example Usage:

query = {
    "name": "run_borzoi_variant_effect",
    "arguments": {
        "ref_sequence": "example_value",
        "alt_sequence": "example_value"
    }
}
result = tu.run(query)