Hey everyone,
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.
Cheers,
André
Hello André,
You may have found this already, but if not, consider decontam:
https://benjjneb.github.io/decontam/vignettes/decontam_intro.html
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!