NCBI Foreign Contamination Screen

sequence-analysis-ncbi-fcs/ncbi-foreign-contamination-screen

Author(s)
National Center for Biotechnology Information
Version
1
Last updated
Apr 16, 2024
License
http://www.usa.gov/publicdomain/label/1.0/
Tags
NCBI

Features
Tutorial
Screening assembled genomes for contamination using NCBI FCS
Workflow Testing
Tests: ✅
Results: Not yet automated
FAIRness PURL
https://gxy.io/GTN:W00183
RO-Crate logo with flask Download Workflow RO-Crate
Launch in Tutorial Mode
Download 
flowchart TD
  0["ℹ️ Input Dataset\nInput genome"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["FCS-GX screen"];
  0 -->|output| 1;
  9741edf2-4be6-45a3-980d-99b1aea18380["Output\nfcs_gx_action_report"];
  1 --> 9741edf2-4be6-45a3-980d-99b1aea18380;
  style 9741edf2-4be6-45a3-980d-99b1aea18380 stroke:#2c3143,stroke-width:4px;
  ddedd49f-8c57-4e3e-a158-3d66ce12f05c["Output\nfcs_gx_taxonomy_report"];
  1 --> ddedd49f-8c57-4e3e-a158-3d66ce12f05c;
  style ddedd49f-8c57-4e3e-a158-3d66ce12f05c stroke:#2c3143,stroke-width:4px;
  2["FCS-GX clean"];
  1 -->|action_report| 2;
  0 -->|output| 2;
  f3a37b43-d304-4ec0-a023-197c9e0ce2e1["Output\ngx_contam_fasta"];
  2 --> f3a37b43-d304-4ec0-a023-197c9e0ce2e1;
  style f3a37b43-d304-4ec0-a023-197c9e0ce2e1 stroke:#2c3143,stroke-width:4px;
  56716c7c-ac7f-42f7-bbef-62a36b4d3810["Output\ngx_clean_fasta"];
  2 --> 56716c7c-ac7f-42f7-bbef-62a36b4d3810;
  style 56716c7c-ac7f-42f7-bbef-62a36b4d3810 stroke:#2c3143,stroke-width:4px;
  3["FCS-adaptor screen"];
  2 -->|clean_fasta| 3;
  6a4baf46-80b0-4a96-b864-9201fc80cdb7["Output\nfcs_adaptor_report"];
  3 --> 6a4baf46-80b0-4a96-b864-9201fc80cdb7;
  style 6a4baf46-80b0-4a96-b864-9201fc80cdb7 stroke:#2c3143,stroke-width:4px;
  1cad7ab4-a817-436c-9a63-fd4e3c6b4bbb["Output\nadaptor_clean_fasta"];
  3 --> 1cad7ab4-a817-436c-9a63-fd4e3c6b4bbb;
  style 1cad7ab4-a817-436c-9a63-fd4e3c6b4bbb stroke:#2c3143,stroke-width:4px;
  4["FCS-adaptor clean"];
  3 -->|adaptor_report| 4;
  2 -->|clean_fasta| 4;
  0da68570-7490-4087-86c8-739522e1a776["Output\nadaptor_contam_fasta"];
  4 --> 0da68570-7490-4087-86c8-739522e1a776;
  style 0da68570-7490-4087-86c8-739522e1a776 stroke:#2c3143,stroke-width:4px;
  4985eb07-30b0-4872-ab83-52ffeb619900["Output\nfinal_clean_fasta"];
  4 --> 4985eb07-30b0-4872-ab83-52ffeb619900;
  style 4985eb07-30b0-4872-ab83-52ffeb619900 stroke:#2c3143,stroke-width:4px;

Inputs

Input Label
Input dataset Input genome

Outputs

From Output Label
toolshed.g2.bx.psu.edu/repos/iuc/ncbi_fcs_gx/ncbi_fcs_gx/0.5.0+galaxy0 NCBI FCS GX FCS-GX screen
toolshed.g2.bx.psu.edu/repos/iuc/ncbi_fcs_gx/ncbi_fcs_gx/0.5.0+galaxy0 NCBI FCS GX FCS-GX clean
toolshed.g2.bx.psu.edu/repos/richard-burhans/ncbi_fcs_adaptor/ncbi_fcs_adaptor/0.5.0+galaxy0 NCBI FCS Adaptor FCS-adaptor screen
toolshed.g2.bx.psu.edu/repos/iuc/ncbi_fcs_gx/ncbi_fcs_gx/0.5.0+galaxy0 NCBI FCS GX FCS-adaptor clean

Tools

Tool Links
toolshed.g2.bx.psu.edu/repos/iuc/ncbi_fcs_gx/ncbi_fcs_gx/0.5.0+galaxy0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/richard-burhans/ncbi_fcs_adaptor/ncbi_fcs_adaptor/0.5.0+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 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 3cc782f47 2024-04-15 19:43:03 Modify NIH funder. Add workflow license URL
1 05ae375a0 2024-04-10 13:59:37 Suggested tutorial changes. Add workflow test.

For Admins

Installing the workflow tools

wget https://training.galaxyproject.org/training-material/topics/sequence-analysis/tutorials/ncbi-fcs/workflows/NCBI-Foreign-Contamination-Screen.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