AutoCLARK

What does it do?

This process runs CLARK, a metagenomics tool, to determine what species are present in a sample. This is useful if you are unsure what species your sample is, or to check to see if any cross-species contamination occurred (or, obviously, if you have a shotgun metagenomics sample). Lots of detail on CLARK is provided at the CLARK website.

How do I use it?

Subject

In the Subject field, put AutoCLARK. Spelling counts, but case sensitivity doesn't.

Description

In the Description field first specify if you want CLARK to look at raw reads or draft assemblies for species determination. For reads, the first line of your description should be fastq, and for assemblies it should be fasta. Subsequent lines should be the SEQIDs you want CLARK to be looking at.

Example

For an example AutoCLARK, see issue 12819.

Interpreting Results

Once CLARK is complete, a file called abundance.xlsx will be uploaded to Redmine. This file shows the species present for each strain in the request. These results should be interpreted with caution - species that show up with low proportions (less than 1-2 percent) are often not actually there and are just artifacts of the analysis.

How long does it take?

CLARK will usually take 10 to 15 minutes to run, though it may take substantially longer if you requested that a large number of SEQIDs be analyzed.

What can go wrong?

1) Requested SEQIDs are not available. If we can't find some of the SEQIDs that you request, you will get a warning message informing you of it.