Workflows
What is a Workflow?Filters
Domestication of new parts before cloning simulation
Add new parts to your sequences before the cloning simulation and interact with the database.
steps:
input: csv file (without header) : The CSV file should contain the constraints line by line in the first column, along with their associated fragments on each line. This data will be passed to the seq_from_DB tool.
seq_from_DB
- Extract the fragments associated with each constraint from the CSV file.
- Check if all fragments are ...
Generate annotated gb for fragments and add them to DB
Automatically generate annotated GenBank files for your fragments based on your constraints and store them in your database.
steps:
input: GenBank files : If your fragments are not in the database, you can generate GenBank files for each fragment to be used as input for the annotation workflow and then passed to the evaluate_manufacturability tool.
evaluate_manufacturability
- Set the constraints for the annotations. ...
Cloning simulation workflow for sequences present in DB
Run the GoldenGate cloning simulation for a list of constructs in a CSV file and interact with a database
steps:
input: csv file (without header) : The CSV file should contain the constraints line by line in the first column, along with their associated fragments on each line. This data will be passed to the seq_from_DB tool.
seq_from_DB
- Extract the fragments associated with each constraint from the CSV file.
- Check ...
