Query for step 1 - new user

[Sanjeev Sariya]

Hi Clark team,

Thank you for creating this tool. I'm interested to use Clark with my raw reads to investigate if they got contaminated. Organism - Staph. Aureus, Illumina paired end 93 read length. Number of isolates that will be run through clark - 113.

I'm in the process of learning and reading notes from Clark website. For step 1 I'm unable to understand which Fasta file I've to use for:

http://clark.cs.ucr.edu/Overview/

Step 1: Create the discriminative 31-mers of the database you have defined in step 0 (if they do not exist already). This can be done by running the default variant CLARK on the sample of your choice, for example: 

$ ./classify_metagenome.sh -O sample.fa -R result

- Is this step mandatory?

Thanks for your time. :)

--S

[Rachid]

Hello Sanjeev!

Thank you for your interest! 

For the Step 1 (to use CLARK-S), you can use any file to execute this step. 

This step is mandatory if the database of 31-mers was not built before and, in doubt, you should do this step anyway.

Cheers,

Rachid

[Sanjeev Sariya]

Dear Rachid,

Thanks for lightening fast response. Nope, did't create any database with 31-kmer.

For this step (using clark-S), I shall go ahead with a closed genome of E. coli which our lab uses consistently.  :)

classify_metagenome.sh -O reference.fasta -R result

Thanks,

Sanjeev