Storing k-mers without counters

[peter-kanvas]

The version 3.2.0 update says that the "possibility to store only k-mers in the database (no counters)" was implemented; however, I don't see any documentation on how to do this. I m building some very large databases that do not rely on the counters, and I'd benefit from any reduction in the final database size. Thank you!

[marekkokot]

Good question, this should definitely be documented. You need to set -cs1 to your command line.
Are you processing kmc output with kmc_tools? If so, there may be some issue because counter-less kmc databases are not fully handled by kmc_tools as far as I remember. Let me know if it helps.

[peter-kanvas]

Thanks for the quick reply! I tried the setting and it did remove the counters and also prevented kmers_subtract for working. A work around for me could be to do my database subtraction and then use kmc_tools transform compact to remove the counters. If I need to perform operations in the future, I could run kmc_tools transform set_counts to re add the counters.

While I'm here, I'd like to suggest a future functionality for kmc_tools filter. It would be helpful to have the option to return a new database with the counts of all kmers from the starting database in the filtered reads. Right now I have to filter the reads, count all the kmers in the reads, and then intersect with the original database.