I was wondering if there is any kind of database for contaminants that are frequently found in reagents and/or contaminants in 16s amplicon sequencing experiments for mouse and/or human organ samples.
My main goal would be to use this specific database to create a custom BLAST database, and have an initial idea of the amount of possible contaminants present in my samples.
You may have found this already, but if not, consider decontam:
Historically, this topic has been controversial
Check out this thread on contaminants found in negative controls and think carefully
@colinbrislawn thank you for your response!!
I know decontam, I've used it and indeed is a very good option!
My question derives from the fact my samples come from a low biodiversity setting and, so, I expect a considerable amount of sequences are from contaminants. It would be useful to have this database, not to exclude anything but, to "manage expectations".
Anyway, I'll check the thread, thank you!