Comparison of two annotation tools: Helixer and Braker3

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• Import to another server (≥23.0+ only!)

flowchart TD
  0["ℹ️ Input Dataset\nGenome sequence"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Dataset\nAlignments from RNA-seq"];
  style 1 stroke:#2c3143,stroke-width:4px;
  2["ℹ️ Input Dataset\nProtein sequences"];
  style 2 stroke:#2c3143,stroke-width:4px;
  3["Helixer"];
  0 -->|output| 3;
  fe43bcd6-5f99-4fd3-b184-2d6bfb340030["Output\nhelixer output"];
  3 --> fe43bcd6-5f99-4fd3-b184-2d6bfb340030;
  style fe43bcd6-5f99-4fd3-b184-2d6bfb340030 stroke:#2c3143,stroke-width:4px;
  4["Braker3"];
  1 -->|output| 4;
  2 -->|output| 4;
  0 -->|output| 4;
  5["Gffread Helixer annotation"];
  3 -->|output| 5;
  0 -->|output| 5;
  2a62bf04-f621-43d5-9e47-4e8b31c32dca["Output\npredicted proteins Helixer annotation"];
  5 --> 2a62bf04-f621-43d5-9e47-4e8b31c32dca;
  style 2a62bf04-f621-43d5-9e47-4e8b31c32dca stroke:#2c3143,stroke-width:4px;
  6["JBrowse"];
  0 -->|output| 6;
  3 -->|output| 6;
  4 -->|output_gff| 6;
  19976896-9df1-45e4-9c96-89e24ae6e596["Output\noutput"];
  6 --> 19976896-9df1-45e4-9c96-89e24ae6e596;
  style 19976896-9df1-45e4-9c96-89e24ae6e596 stroke:#2c3143,stroke-width:4px;
  7["Gffread Braker3 annotation"];
  4 -->|output_gff| 7;
  0 -->|output| 7;
  15b92c57-fd89-4b7a-a3af-d0e0a3fbc6bf["Output\npredicted proteins Braker3 annotation"];
  7 --> 15b92c57-fd89-4b7a-a3af-d0e0a3fbc6bf;
  style 15b92c57-fd89-4b7a-a3af-d0e0a3fbc6bf stroke:#2c3143,stroke-width:4px;
  8["Busco on predicted proteins from Helixer annotation"];
  5 -->|output_pep| 8;
  9840f766-bbf6-4174-a2b8-2a399064d852["Output\nbusco gff predicted proteins Helixer"];
  8 --> 9840f766-bbf6-4174-a2b8-2a399064d852;
  style 9840f766-bbf6-4174-a2b8-2a399064d852 stroke:#2c3143,stroke-width:4px;
  5a659e48-a36f-4304-9513-006aea416a2e["Output\nbusco image predicted proteins Helixer"];
  8 --> 5a659e48-a36f-4304-9513-006aea416a2e;
  style 5a659e48-a36f-4304-9513-006aea416a2e stroke:#2c3143,stroke-width:4px;
  bebdac0d-c353-49a8-a043-9687c4896c17["Output\nbusco missing predicted proteins Helixer"];
  8 --> bebdac0d-c353-49a8-a043-9687c4896c17;
  style bebdac0d-c353-49a8-a043-9687c4896c17 stroke:#2c3143,stroke-width:4px;
  4e1ca88a-74b9-40d4-b63a-461aece6e3b5["Output\nbusco table predicted proteins Helixer"];
  8 --> 4e1ca88a-74b9-40d4-b63a-461aece6e3b5;
  style 4e1ca88a-74b9-40d4-b63a-461aece6e3b5 stroke:#2c3143,stroke-width:4px;
  790c995e-fb86-4935-83e1-9a5dcbf8bf85["Output\nbusco sum predicted proteins Helixer"];
  8 --> 790c995e-fb86-4935-83e1-9a5dcbf8bf85;
  style 790c995e-fb86-4935-83e1-9a5dcbf8bf85 stroke:#2c3143,stroke-width:4px;
  9["OMArk on predicted proteins from Helixer annotation"];
  5 -->|output_pep| 9;
  462d5c32-3784-4c33-83d5-74da40b7276f["Output\nomark detail sum Helixer annotation"];
  9 --> 462d5c32-3784-4c33-83d5-74da40b7276f;
  style 462d5c32-3784-4c33-83d5-74da40b7276f stroke:#2c3143,stroke-width:4px;
  10["OMArk on predicted proteins from Braker3 annotation"];
  7 -->|output_pep| 10;
  d1eb0367-c708-4794-a256-81dac775776a["Output\nomark sum"];
  10 --> d1eb0367-c708-4794-a256-81dac775776a;
  style d1eb0367-c708-4794-a256-81dac775776a stroke:#2c3143,stroke-width:4px;
  5177eeba-2521-40fc-a9d0-eaabc03639e5["Output\nomark detail sum Braker3 annotation"];
  10 --> 5177eeba-2521-40fc-a9d0-eaabc03639e5;
  style 5177eeba-2521-40fc-a9d0-eaabc03639e5 stroke:#2c3143,stroke-width:4px;
  11["Busco on predicted proteins from Braker3 annotation"];
  7 -->|output_pep| 11;
  37700d39-563f-4add-8b89-e046ff5daa87["Output\nbusco image predicted proteins Braker3"];
  11 --> 37700d39-563f-4add-8b89-e046ff5daa87;
  style 37700d39-563f-4add-8b89-e046ff5daa87 stroke:#2c3143,stroke-width:4px;
  b5b8115d-008f-4f59-966e-0906d8dd7c1d["Output\nbusco gff predicted proteins Braker3"];
  11 --> b5b8115d-008f-4f59-966e-0906d8dd7c1d;
  style b5b8115d-008f-4f59-966e-0906d8dd7c1d stroke:#2c3143,stroke-width:4px;
  52cf5cb7-1b61-461d-9361-9674c4431c72["Output\nbusco sum predicted proteins Braker3"];
  11 --> 52cf5cb7-1b61-461d-9361-9674c4431c72;
  style 52cf5cb7-1b61-461d-9361-9674c4431c72 stroke:#2c3143,stroke-width:4px;
  874c74bc-3417-4b03-b4c5-5547f952cabb["Output\nbusco table predicted proteins Braker3"];
  11 --> 874c74bc-3417-4b03-b4c5-5547f952cabb;
  style 874c74bc-3417-4b03-b4c5-5547f952cabb stroke:#2c3143,stroke-width:4px;
  37c86320-3f6f-4f20-a135-019772ec8db0["Output\nbusco missing predicted proteins Braker3"];
  11 --> 37c86320-3f6f-4f20-a135-019772ec8db0;
  style 37c86320-3f6f-4f20-a135-019772ec8db0 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/comparison-braker-helixer-annotation/workflows/Galaxy-Workflow-Comparison_of_two_annotation_tools__Helixer_and_Braker3.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