Genome annotation with Maker
genome-annotation-annotation-with-maker/main-workflow
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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;
Inputs
Input | Label |
---|---|
Input dataset | EST and/or cDNA |
Input dataset | Protein sequences |
Input dataset | Genome sequence |
Outputs
From | Output | Label |
---|---|---|
toolshed.g2.bx.psu.edu/repos/iuc/fasta_stats/fasta-stats/1.0.1 | Fasta Statistics | |
toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/4.1.4 | Busco | |
toolshed.g2.bx.psu.edu/repos/iuc/jcvi_gff_stats/jcvi_gff_stats/0.8.4 | Genome annotation statistics | |
toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/4.1.4 | Busco | |
toolshed.g2.bx.psu.edu/repos/bgruening/augustus_training/augustus_training/3.3.3 | Train Augustus | |
toolshed.g2.bx.psu.edu/repos/iuc/jcvi_gff_stats/jcvi_gff_stats/0.8.4 | Genome annotation statistics | |
toolshed.g2.bx.psu.edu/repos/iuc/snap_training/snap_training/2013_11_29+galaxy1 | Train SNAP | |
toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/4.1.4 | Busco | |
toolshed.g2.bx.psu.edu/repos/iuc/maker_map_ids/maker_map_ids/2.31.11 | Map annotation ids | |
toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.10+galaxy0 | JBrowse | |
toolshed.g2.bx.psu.edu/repos/devteam/gffread/gffread/2.2.1.2 | gffread | |
toolshed.g2.bx.psu.edu/repos/iuc/jcvi_gff_stats/jcvi_gff_stats/0.8.4 | Genome annotation statistics | |
toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/4.1.4 | Busco |
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
Below are the instructions for importing these workflows directly into your Galaxy server of choice to start using them!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:
Video: Importing a workflow from URL
Version History
Version | Commit | Time | Comments |
---|---|---|---|
12 | e61e9eba4 | 2021-07-09 16:50:50 | Fix workflow |
11 | 106af0888 | 2021-07-09 14:57:57 | Update maker workflow |
10 | 005d964a2 | 2021-01-04 09:29:57 | fix workflows |
9 | 774f2aa37 | 2020-12-31 16:14:33 | update maker tutorial and add a short version |
8 | 667ff3de9 | 2020-01-22 10:59:29 | annotation |
7 | eb4d724e0 | 2020-01-15 10:41:35 | Workflow renaming |
6 | 1a3049ca8 | 2019-05-20 09:14:32 | typos + update workflow |
5 | 2318b970d | 2019-05-09 15:27:27 | udpate workflow |
4 | 361236c41 | 2019-04-04 09:00:14 | Changed format of workflows |
3 | 6eef55b7e | 2019-02-27 18:54:36 | Updated install_tutorial_requirements.sh + minor fixes (#1275) |
2 | bc6d0ddca | 2018-09-11 12:38:25 | jbrowse part |
1 | 7b73f26f8 | 2018-09-10 15:51:07 | update wf |
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