...
Parameter | Description | Defaultvalue |
---|---|---|
Input data | To classify single-end (SE) reads or contigs, received by reads de novo assembly, set this parameter to "SE reads or contigs". | SE reads or skaffoldscontigs |
Classification tool | Use CLARK-l on workstations with limited memory (i.e., "l" for light), this software tool provides precise classification on small metagenomes. It works with a sparse or ''light'' database (up to 4 GB of RAM) while still performing ultra accurate and fast results. | CLARK-l |
Database | A path to the folder with the CLARK database files (-D). | |
Minimum k-mer frequency | Minimum of k-mer frequency/occurrence for the discriminative k-mers (-t). For example, for 1 (or, 2), the program will discard any discriminative k-mer that appear only once (or, less than twice). | 0 |
Mode | Set the mode of the execution (-m):
| Default |
Gap | "Gap" or number of non-overlapping k-mers to pass when creating the database (-п). | 4 |
Load database into memory | Request the loading of database file by memory mapped-file (--ldm). This option accelerates the loading time but it will require an additional amount of RAM significant. This option also allows to load the database in multithreaded-task (see also the "Number of threads" parameter). | False |
Number of threads | Use multiple threads for the classification and, with the "Load database into memory" option enabled, for the loading of the database into RAM (-n). | 8 |
Output file | Specify the output file name. | auto |
Parameters in Workflow File
...