I am using Kraken2 in Galaxy for metagenomic classification. I would like to know whether Kraken2 in Galaxy performs quality filtering (e.g., read trimming, low-quality base removal, chimera removal) before classification or if I need to preprocess my reads separately.
Welcome @Komal_Antaliya
The Kraken2 tool form has some basic confidence and base quality filters it can apply at runtime but all of the read preparation steps like adaptor trimming should be done before using it.
We have several tutorials here walking through example protocols. Each of these includes a templated workflow that you adapt for your own needs. That way everything runs as a batch.
GTN Tutorials for → Kraken2: assign taxonomic labels to sequencing reads
You can also find tutorials by searching here with keywords like tool names or analysis domains.
Hope this helps! 