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 using QIAGEN CLC Genomics Workbench?

1.6. How can I trim and assemble my forward and reverse Sanger sequence for each sample in batch using QIAGEN CLC Genomics Workbench?

The Trim Sequences tool meant for trimming of Sanger data can currently not be utilized in a Workflow, but it will be workflow enabled for the next major release.

If using QIAGEN CLC Genomics Workbench, a work-around to create a "Trim and Assemble Batch Workflow" in the current version (20.x) is to replace the Trim Sequences tool with the Trim Reads tool meant for NGS data.

The major differences between the Trim Reads and Trim Sequences tool, is that the Trim Reads tool does not allow for automatic trimming of vector sequence using UniVec database or trimming based saved sequences, instead it uses a Trim adapter list specifying the sequences to trim. Furthermore, the Trim Reads tool output a new sequence list for which the trimmed parts are removed, rather than adding a trim annotation to the original input sequence. The quality trimming works in the same way for the two tools.

To trim and assemble the sequences, build a Workflow containing the Trim Reads tool followed by the Assemble Sequences tool.

If primer sequences should be trimmed, configure the Trim Reads tool with a Trim adapter list.

In this example the Workflow was configured with a Trim adapter list to remove the gene specific PCR primers from the 5' end and their reverse complement from the 3' end.

 

For information about how to create a Trim adapter list please see the following manual page:

Creating a new Trim adapter list

 

For information about how to run the Workflow in batch please see the related FAQ:

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

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