The loadLayout command loads a layout file to be used for an assembly. The format may be either a SOLiD General Feature Format file (.gff) or a File of Filenames file (.fof). When this command is used, SeqMan NGen still aligns each read from the file to the reference, but uses the information contained within the specified file to determine the overall layout of reads.
| Parameter | Description | Allowed values |
|---|---|---|
| layoutFile | (required) Specifies the directory and file name of the layout file. Both .gff and .fof formats are accepted | [directory/filename enclosed in quotes] |
| templateFile | (required) Specifies the directory and file name of the reference sequence file. | [directory/filename enclosed in quotes] |
Example:
loadLayout
templateFile: “/Library/123_project/template.seq”
layoutFile: “/Library/123_project/layoutfile.gff”
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