Sanger1 : From AB1 to aligned consensus and primers fasta + BLAST

Run Workflow in Galaxy

• Galaxy Main
• Galaxy Australia
• Galaxy France
• Galaxy Europe
• Import to another server (≥23.0+ only!)

flowchart TD
  0["ℹ️ Input Collection\nL sequences Forward"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Collection\nH sequences Reverse"];
  style 1 stroke:#2c3143,stroke-width:4px;
  2["ℹ️ Input Dataset\nLCOI primers"];
  style 2 stroke:#2c3143,stroke-width:4px;
  3["ℹ️ Input Dataset\nHCOI primers"];
  style 3 stroke:#2c3143,stroke-width:4px;
  4["ab1 to FASTQ converter"];
  0 -->|output| 4;
  5["ab1 to FASTQ converter"];
  1 -->|output| 5;
  6["What’s your LCOI primer sequence identifier ?"];
  2 -->|output| 6;
  7["What’s your HCOI primer sequence identifier ?"];
  3 -->|output| 7;
  8["seqtk_trimfq"];
  4 -->|output| 8;
  9["seqtk_trimfq"];
  5 -->|output| 9;
  10["Degap.seqs"];
  6 -->|output| 10;
  11["Degap.seqs"];
  7 -->|output| 11;
  12["Sort collection"];
  8 -->|default| 12;
  13["FASTQ Groomer"];
  9 -->|default| 13;
  14["Reverse-Complement"];
  11 -->|out_fasta| 14;
  15["Reverse-Complement"];
  13 -->|output_file| 15;
  16["Sort collection"];
  15 -->|output| 16;
  17["seqtk_mergepe"];
  12 -->|output| 17;
  16 -->|output| 17;
  18["FASTQ Groomer"];
  17 -->|default| 18;
  19["FASTQ to Tabular"];
  18 -->|output_file| 19;
  20["Tabular-to-FASTA"];
  19 -->|output_file| 20;
  21["Align sequences"];
  20 -->|output| 21;
  22["Consensus sequence from aligned FASTA"];
  21 -->|aligned_sequences| 22;
  23["Merge.files"];
  22 -->|output| 23;
  24["Merge.files"];
  23 -->|output| 24;
  14 -->|output| 24;
  10 -->|out_fasta| 24;
  25["Regex Find And Replace"];
  24 -->|output| 25;
  26["Align sequences"];
  25 -->|out_file1| 26;
  27["NCBI BLAST+ blastn"];
  25 -->|out_file1| 27;
  31c2dd1a-918e-4648-a407-d0e3d7172253["Output\nw_blast_output"];
  27 --> 31c2dd1a-918e-4648-a407-d0e3d7172253;
  style 31c2dd1a-918e-4648-a407-d0e3d7172253 stroke:#2c3143,stroke-width:4px;
  7514514f-809a-4a14-8981-cb08c950b523["Output\nw_consensus_aligned_sequences"];
  27 --> 7514514f-809a-4a14-8981-cb08c950b523;
  style 7514514f-809a-4a14-8981-cb08c950b523 stroke:#2c3143,stroke-width:4px;

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

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:

Version History

For Admins

Installing the workflow tools

wget https://training.galaxyproject.org/training-material/topics/sequence-analysis/tutorials/Manage_AB1_Sanger/workflows/Sanger1_From-AB1-to-aligned-consensus-and-primers-fasta-+-BLAST.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