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?
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 https://training.galaxyproject.org/training-material/topics/metagenomics/. 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.