what kmer size should be used for paired end read data?

jenniferlu717 / Bracken

Bracken (Bayesian Reestimation of Abundance with KrakEN) is a highly accurate statistical method that computes the abundance of species in DNA sequences from a metagenomics sample.

http://ccb.jhu.edu/software/bracken/index.shtml

GNU General Public License v3.0

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what kmer size should be used for paired end read data? #234

Closed gregcaporaso closed 9 months ago

gregcaporaso commented 1 year ago

Hi, If I'm processing paired end 2x150 read data with bracken, should I set the read length to 150 or to 300? Thank you!

jenniferlu717 commented 9 months ago

I would use 150 (the length of one of the mates.)

gregcaporaso commented 9 months ago

Thank you @jenniferlu717!