Training Sanger sequences CHD8

sequence-analysis-Manage_AB1_Sanger/training-sanger-sequences-chd8

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:W00179
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 Dataset\nAOPEP_and_CHD8_sequences_20220907.zip?download=1"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Dataset\nPrim"];
  style 1 stroke:#2c3143,stroke-width:4px;
  2["Unzip"];
  0 -->|output| 2;
  3["Filter FASTA"];
  1 -->|output| 3;
  4["Filter FASTA"];
  1 -->|output| 4;
  5["Extract element identifiers"];
  2 -->|unzipped| 5;
  6["Degap.seqs"];
  3 -->|output| 6;
  7["Degap.seqs"];
  4 -->|output| 7;
  8["Regex Find And Replace"];
  5 -->|output| 8;
  9["Regex Find And Replace"];
  5 -->|output| 9;
  10["Reverse-Complement"];
  7 -->|out_fasta| 10;
  11["Filter collection"];
  8 -->|out_file1| 11;
  2 -->|unzipped| 11;
  12["Filter collection"];
  9 -->|out_file1| 12;
  11 -->|output_discarded| 12;
  13["ab1 to FASTQ converter"];
  11 -->|output_filtered| 13;
  14["ab1 to FASTQ converter"];
  12 -->|output_filtered| 14;
  15["seqtk_trimfq"];
  13 -->|output| 15;
  16["seqtk_trimfq"];
  14 -->|output| 16;
  17["FASTQ Groomer"];
  15 -->|default| 17;
  18["Sort collection"];
  16 -->|default| 18;
  19["Sort collection"];
  17 -->|output_file| 19;
  20["Reverse-Complement"];
  19 -->|output| 20;
  21["seqtk_mergepe"];
  18 -->|output| 21;
  20 -->|output| 21;
  22["FASTQ Groomer"];
  21 -->|default| 22;
  23["FASTQ to Tabular"];
  22 -->|output_file| 23;
  24["Tabular-to-FASTA"];
  23 -->|output_file| 24;
  25["Align sequences"];
  24 -->|output| 25;
  26["Consensus sequence from aligned FASTA"];
  25 -->|aligned_sequences| 26;
  27["Merge.files"];
  26 -->|output| 27;
  28["Merge.files"];
  27 -->|output| 28;
  10 -->|output| 28;
  6 -->|out_fasta| 28;
  29["Regex Find And Replace"];
  28 -->|output| 29;
  30["Align sequences"];
  29 -->|out_file1| 30;
  31["NCBI BLAST+ blastn"];
  29 -->|out_file1| 31;

Inputs

Input Label
Input dataset AOPEP_and_CHD8_sequences_20220907.zip?download=1
Input dataset Prim

Outputs

From Output Label
toolshed.g2.bx.psu.edu/repos/devteam/fastx_reverse_complement/cshl_fastx_reverse_complement/1.0.2+galaxy0 Reverse-Complement

Tools

Tool Links
__FILTER_FROM_FILE__
__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/imgteam/unzip/unzip/6.0+galaxy0 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/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 9b2a39983 2024-01-02 11:11:58 Update workflow
1 1d51e2dc3 2023-12-19 13:35:27 Move files from ecology to sequence analysis

For Admins

Installing the workflow tools

wget https://training.galaxyproject.org/training-material/topics/sequence-analysis/tutorials/Manage_AB1_Sanger/workflows/Training-Sanger-sequences-CHD8.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