What is the difference between paired reads or single reads with kraken2 annotation

[timeresistance1996]

For paired reads, is there reads merge before annotation or any operation difference with the single reads?

[jenniferlu717]

For paired reads, Kraken concatenates each pair but placed an "x" inbetween

There is no kmer matching in the overlap but the overall read assignment is now based on kmers from both mates.

[timeresistance1996]

Understood, thank you for the reply!