HomeCLC FAQ - Workflows, Batching and other Workbench utilitiesRunning analyses in batchesHow can I trim and assemble my forward and reverse Sanger sequence for each sample in batch?

1.5. How can I trim and assemble my forward and reverse Sanger sequence for each sample in batch?

1. Trim in batch

To trim several Sanger sequences at the same time, select all sequences as input for the Trim Sequences tool. This is easiest done using the right-click option "Add folder contents" in the wizard.

The Trim Sequences tool will add annotations to the input sequences that signifies the trimmed regions.

 

2. Assemble in batch

To assemble the sequences, build a Workflow containing only the Assemble Sequences element.

 

Create a metadata table in Excel that defines the two Sanger sequences to assemble.

In it's simplest form the metadata only need to include the sequence name (or a unique prefix) and sample name, with two sequences being from the same sample.

 

However, it is also possible to add additional metadata information that you wish to store for the sequences.

 

 

To run the Assemble Sequences Workflow, follow these steps:

  • Launch the Workflow
  • Click the "Batch "option and select the folder with the sequences to assemble

 

  • In the next step select the option "Use metadata"
  • Navigate to the Excel sheet with the metadata by clicking on the folder to the right
  • Select the column to define the batch units on. In this case it is "Sample", but it can be named anything you like

  • In the next step you see an overview of the batch units

In the "Result handling" step you can choose to "Create subfolders per batch unit"

  • If selecting this option subfolders named based on the batch identifier (sample names in this example) will be created
  • The actual contig will be named based on the configuration of the workflow output name. In the example below default naming is used

In the "Result handling" step you can also choose to create a "Workflow Result Metadata". This can be used to navigate to a specific contig and save information about the sample. Additional information can be added to the "Workflow Result Metadata" after it is saved in the "Navigation Area".

 

Relevant manual pages for more details are:

 

Known limitations

  • It is currently not possible to use the Trim Sequences tool in a Workflow. This will be included for a future release of the Workbench.
  • It is currently only possible to name subfolders based on the batch identifier in the metadata. However, the output contigs can be renamed based on the folder name using the Batch Rename tool.

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