I have some shotgun metagenomics data (long reads sequenced by ONT).
I want to use those metagenomics data in order to detect the presence of a specific gene (Cyp51) or its mutated homologous.
I am a little bit confused because I had many ideas in my mind: write a Python code to detect the gene with a certain threshold of similarity, using classifiers like Kraken2 with a specific database containing the ref seq of the gene, BLAST, assembly then annotation, or just use specific tools (I didn't find the one until now)
Anyway, I wanna hear to ur opinions. if you were in my place, what is the strategy and tools that you would work with? Are there specific tools or pipelines that I can use directly, or anything that can help me?
Thanks in advance.
Have a good day