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Candidate Validation

AAV PacBio Quality Control

Assess the completeness and contamination of PacBio sequenced adeno-associated virus (AAV) constructs by examining alignment coverage across sequences and among specific regions including the promoter and CDS.

Runtime Estimates

Average: 2 hours 18 minutes based on 15 test runs

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Workflow Walkthrough

  1. Navigate to the AAV PacBio Quality Control workflow on the Form Bio platform. You can use the Gene Therapy or Candidate Validation filters to help you locate the launcher.
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  1. Select version 1.0.6 from the dropdown tab in the top right corner.
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  1. Click “Run Workflow” in the top right corner.
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  1. Launcher Tabs
    1. Upload input data and select the type of sequences and whether Illumina data is included.
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    3. Select AAV design and upload a transfer plasmid FastA sequence and a file describing genomic regions.
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    5. Select reference genome and genome annotation version.
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    7. Select the alignment algorithm and options for packaging/construct sequences.
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    9. Review settings and name the workflow run. We will call this run “Test1”.
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  2. Click Run Workflow in the bottom left corner to begin analysis.

DR GENE

Design and Rank Guides for Editing Nucleotides with Enzymes.

Run time estimate

Average = TBD

Workflow Walkthrough

  1. Navigate to DR GENE workflow on the Form Bio platform. You can search for this workflow using the bar at the top-right corner or by selecting the Genome Editing or Candidate Validation filters on the left-hand side.
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  1. Select  version 2.1.0 from the dropdown menu in the top right corner. Take a moment to review some information about the workflow analysis, inputs, and outputs. When ready to begin, click Run Workflow.
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  3. Select one of three functions, either Genome Editing, Knock-Out, or Off-target search. Depending on your choice, you will be asked to tune certain parameters about the type of experiment to design guides for.
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  5. Provide the necessary input file for your experiment. For Genome Editing this will be an edit table, for knock-out this will be a list of genes, and for off-target search this will be a spacer sequence list.
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  7. For guide design functions, you’ll be asked to tune some parameters related to PCR primers. In most cases, defaults are desirable.
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  9. For some genome editing algorithms, you’ll be asked to tune some additional parameters related to guide design for that specific algorithm.
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  11. Give your workflow a unique name, and take a moment to review the chosen inputs and parameters. When ready to begin, click Run Workflow to submit your analysis.
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Results Walkthrough

  1. Locate your workflow run from the Activity tab, and select it.
  2. On this page, you can view a variety of information about the workflow run, including inputs, outputs, and parameters. To view the analysis, click Open Analysis in the top right corner.
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  4. A new tab will open containing sequences of interest for all selected editing experiments. Use the tabs in the top-left corner to navigate.
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Optimize a Nucleotide Sequence

Perform various nucleotide optimizations and gather information on a nucleotide sequence of interest. Currently, three functions are supported: Gene Sequence Optimization to optimize codons and folding energies, Predict RNA/DNA 2D/3D Structure to ascertain the structure of a sequence at a given temperature, and Predict Splice Sites to locate potential splice sites in an optimized nucleotide sequence.

Runtime Estimates

Average = 42 minutes

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Workflow Walkthrough

  1. Navigate to the Optimize a Nucleotide Sequence workflow
  2. Select version 1.0.2 from the dropdown menu
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  4. Click “Run Workflow”
  5. Launcher Tabs
    1. Provide sequence name and raw sequence or files corresponding to the sequence
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    3. Review workflow parameters and name workflow run
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    5. Click “Run Workflow”
    6. Results Walkthrough

    7. To view results, first locate your run in the Activity tab. Once found, select it to view more information. On this page, you can view information about the workflow status, analysis outputs, files input and output, parameters, and Nextflow logs.
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    9. Select Analysis from the tabs to view the results of the workflow run. You may also click View Full Screen Results to open the results in a new tab.
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