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Input data

To classify single-end (SE) reads or scaffoldscontigs, received by reads de novo assembly, set this parameter to "SE reads or scaffoldscontigs".
To classify paired-end (PE) reads, set the value to "PE reads".

SE reads or skaffolds
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.


A path to the folder with the CLARK database files (-D).
It is assumed that "targets.txt" file is located in this folder (the file is passed to the "" script from the CLARK package via parameter -T).

Minimum k-mer frequencyMinimum 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):

  • "Full" to get detailed results, confidence scores and other statistics.
  • "Default" to get results summary and perform best trade-off between classification speed, accuracy and RAM usage.
  • "Express" to get results summary with the highest speed possible.

"Gap" or number of non-overlapping k-mers to pass when creating the database (-п).

Increase the value if it is required to reduce the RAM usage. Note that this will degrade the sensitivity.

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).

Output file

Specify the output file name.


Parameters in Workflow File


The element has 1 input port:

Name in GUI: Input sequences: 

URL(s) to FASTQ or FASTA file(s) should be provided. In case casethe of SE reads or scaffolds contigs use the "Input URL 1" slot only.

In case of PE reads input "left" reads to "Input URL 1", "right" reads to "Input URL 2". See also the "Input data" parameter of the element.

Name in Workflow File: in


SlotInGUISlot in Workflow FileType
Input URL 1urlstring

The element has 1 output port:

Name in GUI: CLARK Classification: 

A map of sequence names with the associated taxonomy IDs, classified by CLARK.

Name in Workflow File: out


SlotInGUISlot in Workflow FileType
Taxonomy classification data