Embedded Files
The j5 parameters file is a CSV file that contains a list of all of the parameters that controls how j5 designs DNA assemblies. The order of parameter rows does not matter. If a given parameter row is missing from the parameters file, the default j5 parameter value is used. The first line in the file is a header line that does not contain parameter information, but rather just serves to name the columns below.
Parameter Name column fields:
entries must exactly match those shown in the example below.
Value column fields:
entries are (generally-speaking) user-specifiable. If there are discrete allowable choices (e.g. "Genbank" or "FASTA"), or a non-obvious maximum, etc., this is noted in the adjacent Description column field.
Default Value column fields:
The contents of these fields are purely for the benefit of the user, and does not affect the performance of j5 in any way.
Description column fields:
The contents of these fields are purely for the benefit of the user, and does not affect the performance of j5 in any way.
Here is what an example j5 parameters file looks like (stylized for clarity - links to a PDF for better viewing):
Here is the actual example j5 parameters CSV file: j5_parameters.csv
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