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

sequence-analysis-Manage_AB1_Sanger/sanger1-from-ab1-to-aligned-consensus-and-primers-fasta---blast

Author(s)
Coline Royaux
version Version
1
last_modification Last updated
Jan 8, 2024
license License
MIT
galaxy-tags Tags

Features

Tutorial
hands_on Clean and manage Sanger sequences from raw files to aligned consensus
workflow Other workflows associated with this material
Workflow Testing
Tests: ✅
Results: Not yet automated
FAIRness purl PURL
https://gxy.io/GTN:W00178
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\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;

Inputs

Input Label
Input dataset collection L sequences (Forward)
Input dataset collection H sequences (Reverse)
Input dataset LCOI primers
Input dataset HCOI primers

Outputs

From Output Label
toolshed.g2.bx.psu.edu/repos/ecology/ab1_fastq_converter/ab1_fastq_converter/1.20.0 ab1 to FASTQ converter
toolshed.g2.bx.psu.edu/repos/iuc/seqtk/seqtk_trimfq/1.3.1 seqtk_trimfq
toolshed.g2.bx.psu.edu/repos/iuc/seqtk/seqtk_trimfq/1.3.1 seqtk_trimfq
__SORTLIST__ Sort collection
toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5 FASTQ Groomer
toolshed.g2.bx.psu.edu/repos/devteam/fastx_reverse_complement/cshl_fastx_reverse_complement/1.0.2+galaxy0 Reverse-Complement
__SORTLIST__ Sort collection
toolshed.g2.bx.psu.edu/repos/iuc/seqtk/seqtk_mergepe/1.3.1 seqtk_mergepe
toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5 FASTQ Groomer
toolshed.g2.bx.psu.edu/repos/iuc/qiime_align_seqs/qiime_align_seqs/1.9.1.0 Align sequences
toolshed.g2.bx.psu.edu/repos/ecology/aligned_to_consensus/aligned_to_consensus/1.0.0 Consensus sequence from aligned FASTA
toolshed.g2.bx.psu.edu/repos/iuc/mothur_merge_files/mothur_merge_files/1.39.5.0 Merge.files
toolshed.g2.bx.psu.edu/repos/iuc/mothur_merge_files/mothur_merge_files/1.39.5.0 Merge.files
toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regex1/1.0.3 Regex Find And Replace
toolshed.g2.bx.psu.edu/repos/iuc/qiime_align_seqs/qiime_align_seqs/1.9.1.0 Align sequences
toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastn_wrapper/2.10.1+galaxy2 NCBI BLAST+ blastn

Tools

Tool Links
__SORTLIST__
toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5 View in ToolShed
toolshed.g2.bx.psu.edu/repos/devteam/fastq_to_tabular/fastq_to_tabular/1.1.5 View in ToolShed
toolshed.g2.bx.psu.edu/repos/devteam/fastx_reverse_complement/cshl_fastx_reverse_complement/1.0.2+galaxy0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastn_wrapper/2.10.1+galaxy2 View in ToolShed
toolshed.g2.bx.psu.edu/repos/devteam/tabular_to_fasta/tab2fasta/1.1.1 View in ToolShed
toolshed.g2.bx.psu.edu/repos/ecology/ab1_fastq_converter/ab1_fastq_converter/1.20.0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/ecology/aligned_to_consensus/aligned_to_consensus/1.0.0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/galaxyp/filter_by_fasta_ids/filter_by_fasta_ids/2.3 View in ToolShed
toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regex1/1.0.3 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/mothur_degap_seqs/mothur_degap_seqs/1.39.5.0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/mothur_merge_files/mothur_merge_files/1.39.5.0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/qiime_align_seqs/qiime_align_seqs/1.9.1.0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/seqtk/seqtk_mergepe/1.3.1 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/seqtk/seqtk_trimfq/1.3.1 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 bf907f6d3 2024-01-02 10:53:04 Add creator and license
1 03e5a4f54 2023-12-19 15:21:19 Remove colons

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