Training: 16S rRNA Sequencing With Mothur: Main Tutorial

microbiome-mothur-miseq-sop/mothur-miseq-sop

Author(s)

version Version
1
last_modification Last updated
Jan 15, 2024
license License
None Specified, defaults to CC-BY-4.0
galaxy-tags Tags
microbiome

Features

Tutorial
hands_on 16S Microbial Analysis with mothur (extended)

Workflow Testing
Tests: ❌
Results: Not yet automated
FAIRness purl PURL
https://gxy.io/GTN:W00132
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\nInput FASTQ pairs"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Dataset\nsilva.v4.fasta"];
  style 1 stroke:#2c3143,stroke-width:4px;
  10["Count.seqs"];
  8 -->|groups_out| 10;
  9 -->|out_names| 10;
  11["Align.seqs"];
  1 -->|output| 11;
  9 -->|out_fasta| 11;
  12["Summary.seqs"];
  10 -->|seq_count| 12;
  11 -->|out_align| 12;
  13["Screen.seqs"];
  10 -->|seq_count| 13;
  11 -->|out_align| 13;
  14["Filter.seqs"];
  13 -->|fasta_out| 14;
  15["Unique.seqs"];
  14 -->|filteredfasta| 15;
  13 -->|count_out| 15;
  16["Pre.cluster"];
  15 -->|out_fasta| 16;
  15 -->|out_count| 16;
  17["Chimera.vsearch"];
  16 -->|fasta_out| 17;
  16 -->|count_out| 17;
  18["Remove.seqs"];
  17 -->|out_accnos| 18;
  17 -->|out_count| 18;
  16 -->|fasta_out| 18;
  19["Classify.seqs"];
  2 -->|output| 19;
  18 -->|count_out| 19;
  18 -->|fasta_out| 19;
  3 -->|output| 19;
  2["ℹ️ Input Dataset\ntrainset9_032012.pds.fasta"];
  style 2 stroke:#2c3143,stroke-width:4px;
  20["Remove.lineage"];
  18 -->|count_out| 20;
  18 -->|fasta_out| 20;
  19 -->|taxonomy_out| 20;
  21["Get.groups"];
  20 -->|fasta_out| 21;
  20 -->|count_out| 21;
  22["Remove.groups"];
  20 -->|fasta_out| 22;
  20 -->|count_out| 22;
  20 -->|taxonomy_out| 22;
  23["Seq.error"];
  4 -->|output| 23;
  21 -->|count_out| 23;
  21 -->|fasta_out| 23;
  24["Dist.seqs"];
  21 -->|fasta_out| 24;
  25["Cluster.split"];
  22 -->|fasta_out| 25;
  22 -->|count_out| 25;
  22 -->|taxonomy_out| 25;
  26["Cluster"];
  21 -->|count_out| 26;
  24 -->|out_dist| 26;
  27["Make.shared"];
  22 -->|count_out| 27;
  25 -->|otulist| 27;
  28["Classify.otu"];
  22 -->|count_out| 28;
  25 -->|otulist| 28;
  22 -->|taxonomy_out| 28;
  29["Make.shared"];
  21 -->|count_out| 29;
  26 -->|otulist| 29;
  3["ℹ️ Input Dataset\ntrainset9_032012.pds.tax"];
  style 3 stroke:#2c3143,stroke-width:4px;
  30["Summary.single"];
  27 -->|shared| 30;
  31["Count.groups"];
  27 -->|shared| 31;
  32["Dist.shared"];
  27 -->|shared| 32;
  33["Rarefaction.single"];
  27 -->|shared| 33;
  34["Sub.sample"];
  27 -->|shared| 34;
  35["Taxonomy-to-Krona"];
  28 -->|taxonomies| 35;
  36["Rarefaction.single"];
  29 -->|shared| 36;
  37["Tree.shared"];
  32 -->|distfiles| 37;
  38["Heatmap.sim"];
  32 -->|distfiles| 38;
  39["Plotting tool"];
  33 -->|rarefactioncurves| 39;
  4["ℹ️ Input Dataset\nHMP_MOCK.v35.fasta"];
  style 4 stroke:#2c3143,stroke-width:4px;
  40["Venn"];
  34 -->|shared_out| 40;
  41["Make.biom"];
  28 -->|taxonomies| 41;
  5 -->|output| 41;
  34 -->|shared_out| 41;
  42["Krona pie chart"];
  35 -->|outputfile| 42;
  43["Newick Display"];
  37 -->|tre| 43;
  5["ℹ️ Input Dataset\nmouse.dpw.metadata"];
  style 5 stroke:#2c3143,stroke-width:4px;
  6["Make.contigs"];
  0 -->|output| 6;
  7["Summary.seqs"];
  6 -->|fasta| 7;
  8["Screen.seqs"];
  6 -->|fasta| 8;
  6 -->|group| 8;
  9["Unique.seqs"];
  8 -->|fasta_out| 9;

Inputs

Input Label
Input dataset collection Input FASTQ pairs
Input dataset silva.v4.fasta
Input dataset trainset9_032012.pds.fasta
Input dataset trainset9_032012.pds.tax
Input dataset HMP_MOCK.v35.fasta
Input dataset mouse.dpw.metadata

Outputs

From Output Label

Tools

Tool Links
toolshed.g2.bx.psu.edu/repos/crs4/taxonomy_krona_chart/taxonomy_krona_chart/2.6.1.1 View in ToolShed
toolshed.g2.bx.psu.edu/repos/devteam/xy_plot/XY_Plot_1/1.0.2 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/mothur_align_seqs/mothur_align_seqs/1.39.5.0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/mothur_chimera_vsearch/mothur_chimera_vsearch/1.39.5.1 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/mothur_classify_otu/mothur_classify_otu/1.39.5.0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/mothur_classify_seqs/mothur_classify_seqs/1.39.5.0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/mothur_cluster/mothur_cluster/1.39.5.0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/mothur_cluster_split/mothur_cluster_split/1.39.5.0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/mothur_count_groups/mothur_count_groups/1.39.5.0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/mothur_count_seqs/mothur_count_seqs/1.39.5.0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/mothur_dist_seqs/mothur_dist_seqs/1.39.5.0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/mothur_dist_shared/mothur_dist_shared/1.39.5.0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/mothur_filter_seqs/mothur_filter_seqs/1.39.5.0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/mothur_get_groups/mothur_get_groups/1.39.5.0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/mothur_heatmap_sim/mothur_heatmap_sim/1.39.5.0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/mothur_make_biom/mothur_make_biom/1.39.5.0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/mothur_make_contigs/mothur_make_contigs/1.39.5.0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/mothur_make_shared/mothur_make_shared/1.39.5.0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/mothur_pre_cluster/mothur_pre_cluster/1.39.5.0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/mothur_rarefaction_single/mothur_rarefaction_single/1.39.5.0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/mothur_remove_groups/mothur_remove_groups/1.39.5.0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/mothur_remove_lineage/mothur_remove_lineage/1.39.5.0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/mothur_remove_seqs/mothur_remove_seqs/1.36.1.0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/mothur_screen_seqs/mothur_screen_seqs/1.39.5.0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/mothur_seq_error/mothur_seq_error/1.39.5.0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/mothur_sub_sample/mothur_sub_sample/1.39.5.0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/mothur_summary_seqs/mothur_summary_seqs/1.39.5.0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/mothur_summary_single/mothur_summary_single/1.39.5.0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/mothur_taxonomy_to_krona/mothur_taxonomy_to_krona/1.0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/mothur_tree_shared/mothur_tree_shared/1.39.5.0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/mothur_unique_seqs/mothur_unique_seqs/1.39.5.0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/mothur_venn/mothur_venn/1.39.5.0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/newick_utils/newick_display/1.6 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
1 0e0a2f2cc 2024-01-10 15:47:09 Rename metagenomics topic to microbiome

For Admins

Installing the workflow tools

wget https://training.galaxyproject.org/training-material/topics/microbiome/tutorials/mothur-miseq-sop/workflows/mothur-miseq-sop.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