shotgun metagenomic kraken2

Hello, I am working on sotgun metagenomic data. I have a few questions for Taxonomic classification. I would be very happy if you could help me.

Should I use K-mer value in Kraken2 tool?

Should Kraken2 inputum be clean data? Should it be assembly data?

I ran kraken using these three parameters. How can I understand the quality and accuracy of my outputs?

Do you have any suggestions for another tool other than kraken2 for taxonomic classification?


Hello @Busrak

Kraken2 is for assigning taxonomic groups to reads. And yes, doing some QA first is a good idea before using any analysis tool.

Help from the tool form is quoted below. Scroll down on the form a bit more to find the associated GTN tutorials with more details/examples.

Or, you can review the tutorials directly The Mothur pipeline is an alternative, and is also covered in the tutorials. You could try both and compare.


What it does

Kraken2 is a taxonomic sequence classifier that assigns taxonomic labels to short DNA reads. It does this by examining the k-mers within a read and querying a database with those k-mers. This database contains a mapping of every k-mer in Kraken’s genomic library to the lowest common ancestor (LCA) in a taxonomic tree of all genomes that contain that k-mer. The set of LCA taxa that correspond to the k-mers in a read are then analyzed to create a single taxonomic label for the read; this label can be any of the nodes in the taxonomic tree. Kraken is designed to be rapid, sensitive, and highly precise.