Genome annotation with Maker

genome-annotation-annotation-with-maker/main-workflow

Author(s)
Anthony Bretaudeau, French National Institute for Agriculture, Food, and Environment (INRAE)
version Version
10
last_modification Last updated
Jul 9, 2021
license License
GPL-3.0-or-later
galaxy-tags Tags
genome-annotation

Features

Tutorial
hands_on Genome annotation with Maker

Workflow Testing
Tests: ❌
Results: Not yet automated
FAIRness purl PURL
https://gxy.io/GTN:W00086
RO-Crate logo with flask Download Workflow RO-Crate Workflowhub cloud with gears logo View on WorkflowHub
Launch in Tutorial Mode question
galaxy-download Download
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"];
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  5["Busco"];
  2 -->|output| 5;
  a15e1214-23a2-484b-9c75-1635fcd61fe3["Output\nBUSCO: short summary"];
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  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;
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  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)"];
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  71d41ce2-e90d-435b-9b64-ab4320524770["Output\nGenome annotation statistics: summary (first round)"];
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  8["gffread"];
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  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"];
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  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"];
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  14["Genome annotation statistics"];
  11 -->|output_gff| 14;
  2 -->|output| 14;
  9def2c6e-fd3c-4969-b5d4-d13c187c1144["Output\nGenome annotation statistics: graphs (second round)"];
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  61f7a150-a4a2-46b1-89f5-2170d466656e["Output\nGenome annotation statistics: summary (second round)"];
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  15["Train SNAP"];
  2 -->|output| 15;
  11 -->|output_gff| 15;
  458887f7-0661-4bde-ab1a-875aac6caed8["Output\nSNAP: trained model"];
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  16["Busco"];
  12 -->|output_exons| 16;
  f52b1b41-0ea5-4384-bd43-4927273c909c["Output\nBusco summary second round"];
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  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"];
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  19["JBrowse"];
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  11 -->|output_evidences| 19;
  17 -->|output_evidences| 19;
  5a38ae83-e177-45f3-aa9f-4c1844584fa5["Output\nJBrowse: report"];
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  20["gffread"];
  18 -->|renamed| 20;
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  52fcac23-b612-4377-a19a-2e3b667a23e3["Output\nGffread: exons"];
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  5c47c25e-0ddb-4ade-a5d0-873ff4add28c["Output\nGffread: translation of cds"];
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  84d9183b-9589-464b-9f82-4dae7f87133e["Output\nGffread: cds"];
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  21["Genome annotation statistics"];
  18 -->|renamed| 21;
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  5a863bd4-10f2-4ac8-81b6-ce8b7f663e42["Output\nGenome annotation statistics: summary (third round)"];
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  22["Busco"];
  20 -->|output_exons| 22;
  0bc78676-eecc-4168-894d-34c4ca07cdf3["Output\nBusco summary final round"];
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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

Tool Links
toolshed.g2.bx.psu.edu/repos/bgruening/augustus_training/augustus_training/3.3.3 View in ToolShed
toolshed.g2.bx.psu.edu/repos/devteam/gffread/gffread/2.2.1.2 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/4.1.4 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/fasta_stats/fasta-stats/1.0.1 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.10+galaxy0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/jcvi_gff_stats/jcvi_gff_stats/0.8.4 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/maker/maker/2.31.11 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/maker_map_ids/maker_map_ids/2.31.11 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/snap_training/snap_training/2013_11_29+galaxy1 View in ToolShed

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