tracknado 0.3.2

CLI library to generate UCSC trackhubs from sequencing data

TrackNado

TrackNado builds UCSC Genome Browser track hubs from local track files and a small table of metadata. Use it when you want a repeatable way to stage bigWig, bigBed, BAM, and annotation tracks for a UCSC hub.

The command-line interface is the simplest way to start. The Python API exposes the same build steps for pipelines and scripts.

Install

pip install tracknado

Build a hub

This example creates a hub for four tracks on hg38.

1. Make an editable metadata table from the files:

   tracknado design \
     -i tracks/*.bw \
     -i tracks/*.bb \
     -o tracks.csv
   

2. Edit tracks.csv. Every row is one track. file_path is required; the other columns describe how the track should appear in the browser.

   file_path,name,ext,assay,cell_type,color
   tracks/k562_ctcf.bw,K562 CTCF,bigWig,ChIP-seq,K562,crimson
   tracks/gm12878_ctcf.bw,GM12878 CTCF,bigWig,ChIP-seq,GM12878,#4169E1
   tracks/k562_atac.bw,K562 ATAC,bigWig,ATAC-seq,K562,darkorange
   tracks/peaks.bb,Called peaks,bigBed,Peaks,All,#464646
   

3. Build and stage the hub:

   tracknado create \
     --metadata tracks.csv \
     --output my_hub \
     --hub-name project_tracks \
     --hub-email [e-mail] \
     --genome-name hg38 \
     --subgroup-by assay \
     --subgroup-by cell_type
   

4. Check the staged hub:

   tracknado validate my_hub
   

my_hub now contains project_tracks.hub.txt, the genome and trackDb files, copied track files, and tracknado_config.json. Publish that directory through a web server, then give UCSC the URL to the .hub.txt file.

Common changes

• Add a top-level folder-like grouping: --supergroup-by assay.
• Give tracks colours from a categorical metadata field: --color-by cell_type.
• Combine related signal tracks in one display: --overlay-by condition.
• Convert BED, GTF, or GFF inputs while building: add --convert --chrom-sizes hg38.chrom.sizes.
• Build an assembly hub for a private genome: add --custom-genome --twobit reference.2bit --organism "Species name".

See the documentation for the complete walkthrough, metadata rules, track layouts, and Python examples.

Python API

import pandas as pd
import tracknado as tn

tracks = pd.read_csv("tracks.csv")
hub = (
    tn.HubBuilder()
    .add_tracks_from_df(tracks)
    .group_by("assay", "cell_type")
    .build(
        name="project_tracks",
        genome="hg38",
        outdir="my_hub",
        hub_email="[e-mail]",
    )
)
hub.stage_hub()

License

TrackNado is distributed under the GNU General Public License v3.