Hello Biostars community,
First of all, my apologies for asking many questions step by step here. I don’t have direct guidance, so I am relying on this platform to learn and improve. Thank you for your patience.
I am currently working on metagenomic data from rhizospheric soil, and my focus is on both prokaryotes and eukaryotes. At the moment, I am running assemblies and trying to figure out the best parameters and tools to obtain a good assembly.
After assembly, my plan is to perform taxonomic classification using both:
Assembly-based approach - to annotate MAGs.
For prokaryotes, I am considering GTDB-Tk.
For eukaryotes, I am exploring tools like Tiara and MetaEuk (still searching for the best options for eukaryotic MAGs).
Read-based approach - here I am very confused. There are k-mer-based, marker gene-based, and protein-level methods, but I am not sure which would be the most suitable to capture both prokaryotes and eukaryotes.
My main doubts:
Which methods are generally recommended for read-based taxonomic classification when both prokaryotes and eukaryotes are present?
Which databases are considered reliable for covering both domains?
Are there tools/workflows that people have found particularly effective for handling whole metagenomes (prokaryotes + eukaryotes)?
If anyone here has experience with such datasets, I would be very grateful for your guidance or suggestions on how to structure this pipeline.
Thank you in advance for your time and help.
