Steven Salzberg

> In the past we have relied upon a separate installation of jellyfish when installing KrakenUniq. This appears no longer to be possible? it should still be possible. We include...

The matches reported by KrakenUniq require only a single 31-bp match. Kraken2 requires a similar match, and just 1 k-mer is enough. However, that's not enough for the default settings...

Nice! Thanks Tomer - we use dustmasker ourselves in our pipeline, but we hadn't built it into Kraken as an option. I highly recommend 'dust'-ing any genomes before running Kraken...

> I need to detect the source of paired reads for a batch of sequencing data, and each time I need to reload the database into memory, the loading speed...

use --preload to make sure it all goes into memory the first time. It won't get kicked out.

> I want to confirm the options again. I added the option --preload > > > $kraken2 --db $DBNAME --threads 60 --output "$out_file" \ > > --report "$report_file" --use-names --preload...

hmm, maybe some of the others will answer but all I can say is what I do - I never run krakenuniq with multiple DBs. Instead, I run it with...

yes that's correct - Krakenuniq uses an array that can only hold values up to 2^31 and there are places in the code that would break if you used longer...

you don't have enough RAM - I don't know how you built a KrakenUniq database for NCBI nt, but that's really enormous. (The Kraken2 DB is smaller but still very...

You probably don't have enough RAM on your computer to load the DB, which forces it to swap. This can take forever (or 100s of times longer). First make sure...