Genome annotation with Braker3

Run Workflow in Galaxy

• Galaxy Australia
• Galaxy France
• Galaxy Europe
• Galaxy Main
• Import to another server (≥23.0+ only!)

flowchart TD
  0["ℹ️ Input Parameter\nBUSCO lineage"];
  style 0 fill:#ded,stroke:#393,stroke-width:4px;
  1["ℹ️ Input Dataset\nGenome sequence masked"];
  style 1 stroke:#2c3143,stroke-width:4px;
  2["ℹ️ Input Dataset\nAlignments from RNA-seq"];
  style 2 stroke:#2c3143,stroke-width:4px;
  3["ℹ️ Input Dataset\nProtein sequences"];
  style 3 stroke:#2c3143,stroke-width:4px;
  4[" Fasta Statistics "];
  1 -->|output| 4;
  4c11da0f-57a5-4751-84f9-c6d4e1325602["Output\nfasta stats genome"];
  4 --> 4c11da0f-57a5-4751-84f9-c6d4e1325602;
  style 4c11da0f-57a5-4751-84f9-c6d4e1325602 stroke:#2c3143,stroke-width:4px;
  5["BUSCO on the genome sequences"];
  1 -->|output| 5;
  0 -->|output| 5;
  88d4ce85-b45d-40a2-85a0-ee4af20b70aa["Output\nbusco table genome"];
  5 --> 88d4ce85-b45d-40a2-85a0-ee4af20b70aa;
  style 88d4ce85-b45d-40a2-85a0-ee4af20b70aa stroke:#2c3143,stroke-width:4px;
  8d39ad7f-b6c7-4b29-b225-c0c9e842f528["Output\nbusco sum genome"];
  5 --> 8d39ad7f-b6c7-4b29-b225-c0c9e842f528;
  style 8d39ad7f-b6c7-4b29-b225-c0c9e842f528 stroke:#2c3143,stroke-width:4px;
  c2f275c1-dc94-4914-a3b2-4683f5f742a3["Output\nbusco image genome"];
  5 --> c2f275c1-dc94-4914-a3b2-4683f5f742a3;
  style c2f275c1-dc94-4914-a3b2-4683f5f742a3 stroke:#2c3143,stroke-width:4px;
  facba50a-b7d0-426a-9fe5-62871940f5c9["Output\nbusco missing genome"];
  5 --> facba50a-b7d0-426a-9fe5-62871940f5c9;
  style facba50a-b7d0-426a-9fe5-62871940f5c9 stroke:#2c3143,stroke-width:4px;
  e44bfb06-31df-434e-bd12-b3ff7aef73ae["Output\nbusco gff genome"];
  5 --> e44bfb06-31df-434e-bd12-b3ff7aef73ae;
  style e44bfb06-31df-434e-bd12-b3ff7aef73ae stroke:#2c3143,stroke-width:4px;
  6["Braker3"];
  2 -->|output| 6;
  3 -->|output| 6;
  1 -->|output| 6;
  4c56d329-a4d3-40e5-b0e7-0062256caf13["Output\nbraker gff"];
  6 --> 4c56d329-a4d3-40e5-b0e7-0062256caf13;
  style 4c56d329-a4d3-40e5-b0e7-0062256caf13 stroke:#2c3143,stroke-width:4px;
  7["GFFRead"];
  6 -->|output_gff| 7;
  1 -->|output| 7;
  68c2a3eb-d2ce-432e-b1a9-e83680eb22d8["Output\npredicted proteins"];
  7 --> 68c2a3eb-d2ce-432e-b1a9-e83680eb22d8;
  style 68c2a3eb-d2ce-432e-b1a9-e83680eb22d8 stroke:#2c3143,stroke-width:4px;
  8["JBrowse"];
  1 -->|output| 8;
  6 -->|output_gff| 8;
  c25c5443-10b5-478f-a04b-26c98383090a["Output\njbrowse"];
  8 --> c25c5443-10b5-478f-a04b-26c98383090a;
  style c25c5443-10b5-478f-a04b-26c98383090a stroke:#2c3143,stroke-width:4px;
  9["BUSCO on the predicted protein sequences"];
  7 -->|output_pep| 9;
  0 -->|output| 9;
  cb6b286c-ba11-48e9-b4dd-96a0e6da011b["Output\nbusco image predicted proteins"];
  9 --> cb6b286c-ba11-48e9-b4dd-96a0e6da011b;
  style cb6b286c-ba11-48e9-b4dd-96a0e6da011b stroke:#2c3143,stroke-width:4px;
  7b588cd3-1d62-487d-979a-3da07e2441c7["Output\nbusco gff predicted proteins"];
  9 --> 7b588cd3-1d62-487d-979a-3da07e2441c7;
  style 7b588cd3-1d62-487d-979a-3da07e2441c7 stroke:#2c3143,stroke-width:4px;
  73725e32-7d72-42a6-b298-2e8c18ecc870["Output\nbusco sum predicted proteins"];
  9 --> 73725e32-7d72-42a6-b298-2e8c18ecc870;
  style 73725e32-7d72-42a6-b298-2e8c18ecc870 stroke:#2c3143,stroke-width:4px;
  54997a8e-0555-42d7-938c-fd8a3fd0caf0["Output\nbusco missing predicted proteins"];
  9 --> 54997a8e-0555-42d7-938c-fd8a3fd0caf0;
  style 54997a8e-0555-42d7-938c-fd8a3fd0caf0 stroke:#2c3143,stroke-width:4px;
  aa85c4a1-7d89-48f1-900a-77508af8d600["Output\nbusco table predicted proteins"];
  9 --> aa85c4a1-7d89-48f1-900a-77508af8d600;
  style aa85c4a1-7d89-48f1-900a-77508af8d600 stroke:#2c3143,stroke-width:4px;

Inputs

Outputs

Tools

To use these workflows in Galaxy you can either click the links to download the workflows, or you can right-click and copy the link to the workflow which can be used in the Galaxy form to import workflows.

Importing into Galaxy

Hands On: Importing a workflow

1. Click on galaxy-workflows-activity Workflows in the Galaxy activity bar (on the left side of the screen, or in the top menu bar of older Galaxy instances). You will see a list of all your workflows
2. Click on galaxy-upload Import at the top-right of the screen
3. Provide your workflow
   • Option 1: Paste the URL of the workflow into the box labelled “Archived Workflow URL”
   • Option 2: Upload the workflow file in the box labelled “Archived Workflow File”
4. Click the Import workflow button

Below is a short video demonstrating how to import a workflow from GitHub using this procedure:

Version History

For Admins

Installing the workflow tools

wget https://training.galaxyproject.org/training-material/topics/genome-annotation/tutorials/braker3/workflows/braker.ga -O workflow.ga
workflow-to-tools -w workflow.ga -o tools.yaml
shed-tools install -g GALAXY -a API_KEY -t tools.yaml
workflow-install -g GALAXY -a API_KEY -w workflow.ga --publish-workflows