Assembly with Flye - upgraded

assembly-largegenome/galaxy-workflow-assembly-with-flye

Author(s)
Anna Syme
Version
2
Last updated
May 8, 2024
License
GPL-3.0-or-later
Tags
LG-WF
GTN

Features
Tutorial
Large genome assembly and polishing
Other workflows associated with this material
Workflow Testing
Tests: ❌
Results: Not yet automated
FAIRness PURL
https://gxy.io/GTN:W00010
RO-Crate logo with flask Download Workflow RO-Crate Workflowhub cloud with gears logo View on (Dev) WorkflowHub
Launch in Tutorial Mode
Download 
flowchart TD
  0["ℹ️ Input Dataset\nlong reads"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["Flye: assembly"];
  0 -->|output| 1;
  3960e31d-7a9e-400c-bb21-f6e47b75e649["Output\nFlye assembly on input dataset(s) (consensus)"];
  1 --> 3960e31d-7a9e-400c-bb21-f6e47b75e649;
  style 3960e31d-7a9e-400c-bb21-f6e47b75e649 stroke:#2c3143,stroke-width:4px;
  e524f295-a957-4c91-838c-f8e98e809b6c["Output\nFlye assembly on input dataset(s) (assembly_graph)"];
  1 --> e524f295-a957-4c91-838c-f8e98e809b6c;
  style e524f295-a957-4c91-838c-f8e98e809b6c stroke:#2c3143,stroke-width:4px;
  48b854e2-dd6e-4345-8d05-09abca6659da["Output\nFlye assembly on input dataset(s) (Graphical Fragment Assembly)"];
  1 --> 48b854e2-dd6e-4345-8d05-09abca6659da;
  style 48b854e2-dd6e-4345-8d05-09abca6659da stroke:#2c3143,stroke-width:4px;
  8672c172-71a7-432c-9679-a8e37f36cf53["Output\nFlye assembly on input dataset(s) (assembly_info)"];
  1 --> 8672c172-71a7-432c-9679-a8e37f36cf53;
  style 8672c172-71a7-432c-9679-a8e37f36cf53 stroke:#2c3143,stroke-width:4px;
  2["Fasta statistics"];
  1 -->|consensus| 2;
  3["Quast genome report"];
  1 -->|consensus| 3;
  17cdf8e0-8ad4-4570-afae-1861934fc678["Output\nQuast on input dataset(s):  HTML report"];
  3 --> 17cdf8e0-8ad4-4570-afae-1861934fc678;
  style 17cdf8e0-8ad4-4570-afae-1861934fc678 stroke:#2c3143,stroke-width:4px;
  4["Bandage image: Flye assembly"];
  1 -->|assembly_gfa| 4;
  e66bd129-146f-48dc-95b8-39a2a1ffb68d["Output\nBandage Image on input dataset(s): Assembly Graph Image"];
  4 --> e66bd129-146f-48dc-95b8-39a2a1ffb68d;
  style e66bd129-146f-48dc-95b8-39a2a1ffb68d stroke:#2c3143,stroke-width:4px;
  5["Bar chart: show contig sizes"];
  1 -->|assembly_info| 5;
  6d0a4e23-d631-4e37-8930-3d22fc91369b["Output\nBar chart showing contig sizes"];
  5 --> 6d0a4e23-d631-4e37-8930-3d22fc91369b;
  style 6d0a4e23-d631-4e37-8930-3d22fc91369b stroke:#2c3143,stroke-width:4px;

Inputs

Input Label
Input dataset long reads

Outputs

From Output Label
toolshed.g2.bx.psu.edu/repos/bgruening/flye/flye/2.9.3+galaxy0 Flye Flye: assembly
toolshed.g2.bx.psu.edu/repos/iuc/quast/quast/5.2.0+galaxy1 Quast Quast genome report
toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_image/2022.09+galaxy4 Bandage Image Bandage image: Flye assembly
barchart_gnuplot Bar chart Bar chart: show contig sizes

Tools

Tool Links
barchart_gnuplot
toolshed.g2.bx.psu.edu/repos/bgruening/flye/flye/2.9.3+galaxy0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_image/2022.09+galaxy4 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/fasta_stats/fasta-stats/2.0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/quast/quast/5.2.0+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 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
5 f3dd83775 2024-05-07 09:31:40 Update Galaxy-Workflow-Assembly_with_Flye.ga
4 e8ddbcdd5 2024-05-01 04:32:16 new versions of workflows
3 43baea079 2024-05-01 04:20:39 Rename Galaxy-Workflow-Assembly_with_Flye.ga to Galaxy-Workflow-Assembly_with_Flye_old.ga
2 62e77944b 2023-02-17 09:53:23 add/complete creator info on workflows
1 9fcb3aeec 2022-10-07 06:24:16 large genome tutorial

For Admins

Installing the workflow tools

wget https://training.galaxyproject.org/training-material/topics/assembly/tutorials/largegenome/workflows/Galaxy-Workflow-Assembly_with_Flye.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