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|
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.
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).
Set the mode of the execution (-m):
"Gap" or number of non-overlapping k-mers to pass when creating the database (-п).
|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).
|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).
Specify the output file name.
Parameters in Workflow File