Form Bio Platform Documentation
Form Bio Platform Documentation
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Genomics

16S Sequencing

Perform taxonomic classification on 16S sequencing data

Runtime Estimates

TBD

Workflow Walkthrough

  1. Navigate to the 16S Sequencing Analysis launcher card. This can also be found using the search bar at the top right, or using the “Genomics” tag on the left-hand side.
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  2. Select version 1.0.0 from the dropdown bar on the top right side.
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  3. Click “Run Workflow” in the top right corner.
  4. Launcher Tabs
    1. Select the algorithm (MOTHUR or QIIME) and select the file directory for the input reads
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    2. Provide a sample attribute file relating run IDs and sample IDs
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      c. Name the workflow, and review workflow parameters. When you are satisfied, click “Run Workflow” at the bottom right corner

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Genome Assembly

Assemble genomes from short and/or long-read sequencing data

Workflow Walkthrough

  1. Navigate to the Genome Assembly workflow on the Form Bio platform. You can use the search bar in the top right corner or use the Genomics filter on the left-hand side to help navigate to this workflow.
  2. Select version 1.0.2 from the drop-down versioning menu, and review information about the workflow. When ready to begin, click Run Workflow
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  3. Select the type of input data (ONT, PacBio, Illumina, etc) and provide these files as input. Some input data types, like ONT, support basecalling, and you will be asked to choose the algorithm to run basecalling with.
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  4. If applicable, choose how basecalling is performed and tune additional parameters based on your chosen algorithm.
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  5. If applicable, choose the type of polishing algorithm to run and tune additional parameters based on your chosen algorithm.
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  6. Choose an assembly algorithm. The algorithm options and input parameters may differ based on your input sequencing data type.
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  7. Most runs will require you to choose an evaluation algorithm. Certain evaluation algorithms may require additional parameters, such as lineage or reference assembly.
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  8. Give your workflow run a unique name and review all the inputs and parameters. When ready to submit workflow, click “Run Workflow”
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Results Walkthrough

  1. To view the results of your Genome Assembly workflow run, first find and select your workflow run from the Activity tab.
  2. Navigate to the Files tab. Here, under output, all analysis files will be nested.
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Genome Coordinate Conversion

Convert the location of a set of genomic features, such as genes, transcription factor bindings sites, or promoters, from one genome to another

Workflow Walkthrough

  1. Navigate to the Genome Coordinate Conversion workflow on the Form Bio platform. This workflow can also be found using the search bar at the top right or by selecting either the “Genomics” or “Sequence Alignment” filter.
  2. On the launcher page, you can view use-cases, a brief summary of the analysis, and information on inputs and outputs of the workflow. When ready to begin, click Run Workflow in the top right corner.
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  3. On the inputs tab, select the type of analysis you wish to perform - either creation of a Genome Coordinate Conversion File, or the conversion of genomic regions using a preexisting file. Then, upload the query and target genomes as FastA files.
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  4. Review the workflow parameters and file inputs. Give your workflow run a unique name. When ready to submit the job, click Run Workflow at the bottom right corner.
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Results Walkthrough

  1. To view the results of your Genome Coordinate Conversion workflow, first find and select your workflow run from the Activity tab.
  2. Navigate to the Files tab. Under output, all workflow files will be listed. You may also view these files in the File Explorer on the left-hand side.

FLAG: Eukaryote Genome Annotation

Annotate eukaryote genomes from an input FastA file

Workflow Walkthrough

  1. Navigate to the FLAG: Eukaryote Gene Annotation workflow on the Form Bio platform. You can find the workflow using the search bar on the top right or by using the Genomics filter on the left-hand side.
  2. Take a moment to view information on inputs, outputs, and a workflow summary. Select version 2.0.0 from the dropdown launcher. When ready to begin, click Run Workflow
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  3. Start by providing the scientific name of the species to annotate, formatted with a space between the species and genus - drosophila_melanogaster, for example. Then, upload FastA files corresponding to the genome, proteins, and RNA. Choose whether to softmask the input files.
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  4. For finding homologous proteins, select whether to search for transcripts or proteins - generally just searching for transcripts is recommended. Then, select the database to search, such as RefSeq.
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  5. Tune some parameters related to the size of the genome, and which gene prediction algorithms to use. You may also additionally provide a related organism genome assembly and annotation file.
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  6. Take a moment to review workflow inputs and parameters. Give your workflow run a unique name, then click Run Workflow to submit for analysis.

Results Walkthrough

  1. To view the results of your FLAG run, first locate and select your workflow run from the Activity tab of the Form Bio platform.
  2. Select the Files tab and navigate to the outputs nested folder. All workflow analysis files will be here. You can also view these files through the File Explorer.
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Prokaryotic (Meta)Genome Analysis

Workflow Walkthrough

  1. Navigate to the ProkGenoRanger: Prokaryotic (Meta)Genome Analysis workflow on the Form Bio platform. You can use the Genomics filter on the left-hand side to help find this workflow.
  2. Select version 1.0.0 from the dropdown versioning menu in the top-right corner. You can view some information about the workflow inputs and parameters on this page. When ready to begin, click Run Workflow.
  3. Select the data type you wish to analyze. Currently, there are three supported functions: 16s rRNA analysis, Single-Genome Analysis, and Metagenome Assembly. Then, provide your input data and a sample attribute file. There may be additional inputs required based on your input data type.
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  4. Edit additional parameters based on your input data, including the analysis algorithm, polishing algorithm, and minimum read/contig lengths. These parameters may differ based on your chosen data type.
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  5. Give your workflow run a unique name, and then review the inputs and parameters associated with your analysis. When ready to submit the run, click Run Workflow.

Results Walkthrough

  1. To view the results of your ProkGenoRanger workflow, first find and select your workflow run from the Activity tab.
  2. Navigate to the Files tab, then output. All files associated with your workflow run will be present here.
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