Genome annotation with Maker

Run Workflow in Galaxy

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

flowchart TD
  0["ℹ️ Input Dataset\nEST and/or cDNA"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Dataset\nProtein sequences"];
  style 1 stroke:#2c3143,stroke-width:4px;
  2["ℹ️ Input Dataset\nGenome sequence"];
  style 2 stroke:#2c3143,stroke-width:4px;
  3["Maker"];
  0 -->|output| 3;
  2 -->|output| 3;
  1 -->|output| 3;
  4["Fasta Statistics"];
  2 -->|output| 4;
  2d3829e6-f5b9-46d1-83e3-17efff814e09["Output\nFasta Statistics on input dataset(s): Fasta summary stats"];
  4 --> 2d3829e6-f5b9-46d1-83e3-17efff814e09;
  style 2d3829e6-f5b9-46d1-83e3-17efff814e09 stroke:#2c3143,stroke-width:4px;
  5["Busco"];
  2 -->|output| 5;
  a15e1214-23a2-484b-9c75-1635fcd61fe3["Output\nBUSCO: short summary"];
  5 --> a15e1214-23a2-484b-9c75-1635fcd61fe3;
  style a15e1214-23a2-484b-9c75-1635fcd61fe3 stroke:#2c3143,stroke-width:4px;
  7806088d-f657-4389-9d54-6a3bdfa233b2["Output\nBUSCO: list of missing ortholog genes"];
  5 --> 7806088d-f657-4389-9d54-6a3bdfa233b2;
  style 7806088d-f657-4389-9d54-6a3bdfa233b2 stroke:#2c3143,stroke-width:4px;
  6a27d0f6-d83c-42b1-a7af-5f99ba5debe2["Output\nBUSCO: full table"];
  5 --> 6a27d0f6-d83c-42b1-a7af-5f99ba5debe2;
  style 6a27d0f6-d83c-42b1-a7af-5f99ba5debe2 stroke:#2c3143,stroke-width:4px;
  6["Train Augustus"];
  2 -->|output| 6;
  3 -->|output_gff| 6;
  7["Genome annotation statistics"];
  3 -->|output_gff| 7;
  2 -->|output| 7;
  2bed9aa6-5f22-494d-9caa-f0ece8464f15["Output\nGenome annotation statistics: graphs (first round)"];
  7 --> 2bed9aa6-5f22-494d-9caa-f0ece8464f15;
  style 2bed9aa6-5f22-494d-9caa-f0ece8464f15 stroke:#2c3143,stroke-width:4px;
  71d41ce2-e90d-435b-9b64-ab4320524770["Output\nGenome annotation statistics: summary (first round)"];
  7 --> 71d41ce2-e90d-435b-9b64-ab4320524770;
  style 71d41ce2-e90d-435b-9b64-ab4320524770 stroke:#2c3143,stroke-width:4px;
  8["gffread"];
  3 -->|output_gff| 8;
  2 -->|output| 8;
  9["Train SNAP"];
  2 -->|output| 9;
  3 -->|output_gff| 9;
  10["Busco"];
  8 -->|output_exons| 10;
  a79ab19d-9802-42ca-8ffa-8c197a16c8b8["Output\nBusco summary first round"];
  10 --> a79ab19d-9802-42ca-8ffa-8c197a16c8b8;
  style a79ab19d-9802-42ca-8ffa-8c197a16c8b8 stroke:#2c3143,stroke-width:4px;
  11["Maker"];
  6 -->|output_tar| 11;
  9 -->|output| 11;
  2 -->|output| 11;
  3 -->|output_full| 11;
  12["gffread"];
  11 -->|output_gff| 12;
  2 -->|output| 12;
  13["Train Augustus"];
  2 -->|output| 13;
  11 -->|output_gff| 13;
  42d5aadd-3a8c-441d-913f-ee8745a99b0b["Output\nAugus: trained model"];
  13 --> 42d5aadd-3a8c-441d-913f-ee8745a99b0b;
  style 42d5aadd-3a8c-441d-913f-ee8745a99b0b stroke:#2c3143,stroke-width:4px;
  14["Genome annotation statistics"];
  11 -->|output_gff| 14;
  2 -->|output| 14;
  9def2c6e-fd3c-4969-b5d4-d13c187c1144["Output\nGenome annotation statistics: graphs (second round)"];
  14 --> 9def2c6e-fd3c-4969-b5d4-d13c187c1144;
  style 9def2c6e-fd3c-4969-b5d4-d13c187c1144 stroke:#2c3143,stroke-width:4px;
  61f7a150-a4a2-46b1-89f5-2170d466656e["Output\nGenome annotation statistics: summary (second round)"];
  14 --> 61f7a150-a4a2-46b1-89f5-2170d466656e;
  style 61f7a150-a4a2-46b1-89f5-2170d466656e stroke:#2c3143,stroke-width:4px;
  15["Train SNAP"];
  2 -->|output| 15;
  11 -->|output_gff| 15;
  458887f7-0661-4bde-ab1a-875aac6caed8["Output\nSNAP: trained model"];
  15 --> 458887f7-0661-4bde-ab1a-875aac6caed8;
  style 458887f7-0661-4bde-ab1a-875aac6caed8 stroke:#2c3143,stroke-width:4px;
  16["Busco"];
  12 -->|output_exons| 16;
  f52b1b41-0ea5-4384-bd43-4927273c909c["Output\nBusco summary second round"];
  16 --> f52b1b41-0ea5-4384-bd43-4927273c909c;
  style f52b1b41-0ea5-4384-bd43-4927273c909c stroke:#2c3143,stroke-width:4px;
  17["Maker"];
  13 -->|output_tar| 17;
  15 -->|output| 17;
  2 -->|output| 17;
  11 -->|output_full| 17;
  18["Map annotation ids"];
  17 -->|output_gff| 18;
  63575dcf-54d1-4cb1-b5fb-a2810b4da807["Output\nMap annotation ids: renamed GFF"];
  18 --> 63575dcf-54d1-4cb1-b5fb-a2810b4da807;
  style 63575dcf-54d1-4cb1-b5fb-a2810b4da807 stroke:#2c3143,stroke-width:4px;
  19["JBrowse"];
  2 -->|output| 19;
  3 -->|output_gff| 19;
  18 -->|renamed| 19;
  11 -->|output_gff| 19;
  3 -->|output_evidences| 19;
  11 -->|output_evidences| 19;
  17 -->|output_evidences| 19;
  5a38ae83-e177-45f3-aa9f-4c1844584fa5["Output\nJBrowse: report"];
  19 --> 5a38ae83-e177-45f3-aa9f-4c1844584fa5;
  style 5a38ae83-e177-45f3-aa9f-4c1844584fa5 stroke:#2c3143,stroke-width:4px;
  20["gffread"];
  18 -->|renamed| 20;
  2 -->|output| 20;
  52fcac23-b612-4377-a19a-2e3b667a23e3["Output\nGffread: exons"];
  20 --> 52fcac23-b612-4377-a19a-2e3b667a23e3;
  style 52fcac23-b612-4377-a19a-2e3b667a23e3 stroke:#2c3143,stroke-width:4px;
  5c47c25e-0ddb-4ade-a5d0-873ff4add28c["Output\nGffread: translation of cds"];
  20 --> 5c47c25e-0ddb-4ade-a5d0-873ff4add28c;
  style 5c47c25e-0ddb-4ade-a5d0-873ff4add28c stroke:#2c3143,stroke-width:4px;
  84d9183b-9589-464b-9f82-4dae7f87133e["Output\nGffread: cds"];
  20 --> 84d9183b-9589-464b-9f82-4dae7f87133e;
  style 84d9183b-9589-464b-9f82-4dae7f87133e stroke:#2c3143,stroke-width:4px;
  21["Genome annotation statistics"];
  18 -->|renamed| 21;
  2 -->|output| 21;
  f5d4a6bf-1ff8-435a-8084-7921e25bff3a["Output\nGenome annotation statistics: graphs (third round)"];
  21 --> f5d4a6bf-1ff8-435a-8084-7921e25bff3a;
  style f5d4a6bf-1ff8-435a-8084-7921e25bff3a stroke:#2c3143,stroke-width:4px;
  5a863bd4-10f2-4ac8-81b6-ce8b7f663e42["Output\nGenome annotation statistics: summary (third round)"];
  21 --> 5a863bd4-10f2-4ac8-81b6-ce8b7f663e42;
  style 5a863bd4-10f2-4ac8-81b6-ce8b7f663e42 stroke:#2c3143,stroke-width:4px;
  22["Busco"];
  20 -->|output_exons| 22;
  0bc78676-eecc-4168-894d-34c4ca07cdf3["Output\nBusco summary final round"];
  22 --> 0bc78676-eecc-4168-894d-34c4ca07cdf3;
  style 0bc78676-eecc-4168-894d-34c4ca07cdf3 stroke:#2c3143,stroke-width:4px;

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

• Click on Workflow on the top menu bar of Galaxy. You will see a list of all your workflows.
• Click on galaxy-upload Import at the top-right of the screen
• 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”
• 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/annotation-with-maker/workflows/main_workflow.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