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Impact of k-mer length for kraken2 database

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?

sequence
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updated by Dave • Dave • written by josmos43 • josmos43

1 answer

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

--memory-mapping

To avoid loading all your database into RAM.

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written by Dave • Dave

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