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DerrickWood / kraken2

The second version of the Kraken taxonomic sequence classification system
MIT License
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can kraken2 be use to Identify species in WGBS reads ？ #298

Open feihongloveworld opened 4 years ago

feihongloveworld commented 4 years ago

hi sir; kraken2 is a perfect tools for identify species in metagenomic data. there are many WGBS reads from human WGBS project ，which want to identity Possible pathogen； can kraken2 do it ？ thanks

jenniferlu717 commented 4 years ago

Technically yes, but it may fail to classify properly. I'm not going to go into the details of it all, but you may have some problem classifying reads unless you pre-treated the reference by converting Cs to Ts. In the WGBS reads, the unmethylated cytosines become Ts and the kmers no longer will match the database.