Impact of k-mer length for kraken2 database

Question

[josmos43]

I am analysing 125bp paired-end metagenomic data, using kraken2 for taxonomic classification. I am running into memory issues, since I am using a very large custom Database. The size of the database is significantly decreased without removing sequences, when I increase the k-mer length. Currently i am using a value of 43 instead of the default of 35. I don't know how this is going to affect my results. The documentation does not give any clear information about this issue. Is it save to increase this value or should I rather remove some sequences to reduce the database size?

Answer 1

[Dave]

If you are having memory issues, you can add this flag to your command:

--memory-mapping

To avoid loading all your database into RAM.