Building an amplicon sequence variant (ASV) table from 16S data using DADA2

microbiome-dada-16S/workflow

Author(s)
, Bérénice Batut
version Version
1
last_modification Last updated
Jun 5, 2024
license License
MIT
galaxy-tags Tags
microbiome

Features

Tutorial
hands_on Building an amplicon sequence variant (ASV) table from 16S data using DADA2

Workflow Testing
Tests: ✅
Results: Not yet automated
FAIRness purl PURL
https://gxy.io/GTN:W00122
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 Collection\nRaw reads"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Dataset\nheader"];
  style 1 stroke:#2c3143,stroke-width:4px;
  2["Sort collection"];
  0 -->|output| 2;
  3["dada2: filterAndTrim"];
  2 -->|output| 3;
  4["dada2: plotQualityProfile"];
  2 -->|output| 4;
  5["Unzip collection"];
  3 -->|paired_output| 5;
  6["dada2: plotQualityProfile"];
  3 -->|paired_output| 6;
  7["dada2: learnErrors"];
  5 -->|forward| 7;
  8["dada2: learnErrors"];
  5 -->|reverse| 8;
  9["dada2: dada"];
  5 -->|forward| 9;
  7 -->|errors| 9;
  10["dada2: dada"];
  5 -->|reverse| 10;
  8 -->|errors| 10;
  11["dada2: mergePairs"];
  9 -->|data_collection| 11;
  10 -->|data_collection| 11;
  5 -->|forward| 11;
  5 -->|reverse| 11;
  12["Extract element identifiers"];
  11 -->|merged| 12;
  13["dada2: makeSequenceTable"];
  11 -->|merged| 13;
  3fd25979-39df-4698-bad1-aabfccbb7bd2["Output\nsequence_table"];
  13 --> 3fd25979-39df-4698-bad1-aabfccbb7bd2;
  style 3fd25979-39df-4698-bad1-aabfccbb7bd2 stroke:#2c3143,stroke-width:4px;
  14["Replace Text"];
  12 -->|output| 14;
  15["dada2: removeBimeraDenovo"];
  13 -->|stable| 15;
  16["Select first"];
  14 -->|outfile| 16;
  17["dada2: sequence counts"];
  3 -->|outtab| 17;
  9 -->|data_collection| 17;
  10 -->|data_collection| 17;
  11 -->|merged| 17;
  15 -->|stable_sequencetable| 17;
  c758f861-44bc-4208-b1f7-1f5106cb678e["Output\nsequence_counts"];
  17 --> c758f861-44bc-4208-b1f7-1f5106cb678e;
  style c758f861-44bc-4208-b1f7-1f5106cb678e stroke:#2c3143,stroke-width:4px;
  18["dada2: assignTaxonomy and addSpecies"];
  15 -->|stable_sequencetable| 18;
  904fe0a2-8329-45ca-8493-fc688fb216c3["Output\ntaxons"];
  18 --> 904fe0a2-8329-45ca-8493-fc688fb216c3;
  style 904fe0a2-8329-45ca-8493-fc688fb216c3 stroke:#2c3143,stroke-width:4px;
  19["Compute"];
  16 -->|outfile| 19;
  20["Replace Text"];
  19 -->|out_file1| 20;
  21["Concatenate datasets"];
  1 -->|output| 21;
  20 -->|outfile| 21;
  5479d320-3e82-47a9-a92b-6ed5959459cf["Output\nmetada_table"];
  21 --> 5479d320-3e82-47a9-a92b-6ed5959459cf;
  style 5479d320-3e82-47a9-a92b-6ed5959459cf stroke:#2c3143,stroke-width:4px;
  22["Create phyloseq object"];
  21 -->|out_file1| 22;
  15 -->|stable_sequencetable| 22;
  18 -->|output| 22;

Inputs

Input Label
Input dataset collection Raw reads
Input dataset header

Outputs

From Output Label
toolshed.g2.bx.psu.edu/repos/iuc/dada2_makesequencetable/dada2_makeSequenceTable/1.30.0+galaxy0 dada2: makeSequenceTable
toolshed.g2.bx.psu.edu/repos/iuc/dada2_seqcounts/dada2_seqCounts/1.30.0+galaxy0 dada2: sequence counts
toolshed.g2.bx.psu.edu/repos/iuc/dada2_assigntaxonomyaddspecies/dada2_assignTaxonomyAddspecies/1.30.0+galaxy0 dada2: assignTaxonomy and addSpecies
cat1 Concatenate datasets

Tools

Tool Links
__SORTLIST__
__UNZIP_COLLECTION__
cat1
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_head_tool/9.3+galaxy1 View in ToolShed
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/9.3+galaxy1 View in ToolShed
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/9.3+galaxy1 View in ToolShed
toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/collection_element_identifiers/collection_element_identifiers/0.0.2 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/dada2_assigntaxonomyaddspecies/dada2_assignTaxonomyAddspecies/1.30.0+galaxy0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/dada2_dada/dada2_dada/1.30.0+galaxy0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/dada2_filterandtrim/dada2_filterAndTrim/1.30.0+galaxy0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/dada2_learnerrors/dada2_learnErrors/1.30.0+galaxy0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/dada2_makesequencetable/dada2_makeSequenceTable/1.30.0+galaxy0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/dada2_mergepairs/dada2_mergePairs/1.30.0+galaxy0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/dada2_plotqualityprofile/dada2_plotQualityProfile/1.30.0+galaxy0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/dada2_removebimeradenovo/dada2_removeBimeraDenovo/1.30.0+galaxy0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/dada2_seqcounts/dada2_seqCounts/1.30.0+galaxy0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/phyloseq_from_dada2/phyloseq_from_dada2/1.46.0+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
  • 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
2 97f8a3d0b 2024-06-05 08:50:03 Fix Matthias' comments
1 c1470a165 2024-05-30 13:03:07 Finalize tuto, add workflow+test, rename tuto folder

For Admins

Installing the workflow tools

wget https://training.galaxyproject.org/training-material/topics/microbiome/tutorials/dada-16S/workflows/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