Intro to Genome Assembly

assembly-general-introduction/assembly-general-introduction

Author(s)

Version
5
Last updated
Jul 25, 2020
License
None Specified, defaults to CC-BY-4.0
Tags
assembly

Features
Tutorial
An Introduction to Genome Assembly
Workflow Testing
Tests: ✅
Results: Not yet automated
FAIRness PURL
https://gxy.io/GTN:W00008
RO-Crate logo with flask Download Workflow RO-Crate Workflowhub cloud with gears logo View on (Dev) WorkflowHub
Launch in Tutorial Mode
Download 
output
output
output
output
text_file
text_file
outfile_pairs
out_file1
output
contigs
ℹ️ Input Dataset
mutant_R1.fastq
ℹ️ Input Dataset
mutant_R2.fastq
ℹ️ Input Dataset
wildtype.fna
FastQC
FastQC
FASTQ interlacer
MultiQC
velveth
velvetg
Quast
Output
fastqc_html
Output
fastqc_txt
Output
output_pairs
Output
output_singles
Output
multiqc_stats
Output
multiqc_report
Output
velveth_out
Output
velvet_contigs
Output
velvet_stats
Output
quast_report_html
Output
quast_report_pdf

Inputs

Input Label
Input dataset mutant_R1.fastq
Input dataset mutant_R2.fastq
Input dataset wildtype.fna

Outputs

From Output Label
Input dataset mutant_R1.fastq
Input dataset mutant_R2.fastq
Input dataset wildtype.fna
toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1 FastQC
toolshed.g2.bx.psu.edu/repos/devteam/fastq_paired_end_interlacer/fastq_paired_end_interlacer/1.2.0.1+galaxy0 FASTQ interlacer
toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.7 MultiQC
toolshed.g2.bx.psu.edu/repos/devteam/velvet/velveth/1.2.10.1 velveth
toolshed.g2.bx.psu.edu/repos/devteam/velvet/velvetg/1.2.10.1 velvetg
toolshed.g2.bx.psu.edu/repos/iuc/quast/quast/5.0.2+galaxy0 Quast

Tools

Tool Links
toolshed.g2.bx.psu.edu/repos/devteam/fastq_paired_end_interlacer/fastq_paired_end_interlacer/1.2.0.1+galaxy0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1 View in ToolShed
toolshed.g2.bx.psu.edu/repos/devteam/velvet/velvetg/1.2.10.1 View in ToolShed
toolshed.g2.bx.psu.edu/repos/devteam/velvet/velveth/1.2.10.1 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.7 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/quast/quast/5.0.2+galaxy0 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
  1. Click on 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 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:

Video: Importing a workflow from URL

Version History

Version Commit Time Comments
6 b435b09a4 2020-07-25 07:55:11 updated test for general-introduction, added test for debruijn-graph-assembly using planemo https://github.com/galaxyproject/planemo/pull/1028
5 0f6d81078 2020-02-20 19:19:54 proper version
4 8c24dc774 2020-02-07 17:29:23 intro to assembly workflow updated
3 667ff3de9 2020-01-22 10:59:29 annotation
2 eb4d724e0 2020-01-15 10:41:35 Workflow renaming
1 4d69dccf6 2018-05-22 14:24:00 add new testing files

For Admins

Installing the workflow tools

wget https://training.galaxyproject.org/training-material/topics/assembly/tutorials/general-introduction/workflows/assembly-general-introduction.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