Hello,
I’m interested in running the chimera.slayer command for both bacterial and archaeal 16S pyrosequences. To clarify - is the silva gold template available on the wiki appropriate for archaeal sequences or is it just to be used with bacterial sequences? I’m assuming it is only for bacteria, because the file that downloads is titled silva.gold.bacteria.zip . . . . .
Thanks for your help!
That’s right - it’s only for the Bacteria. As far as I can tell, the sequences in that database were not found to be chimeric by Pintail and are all at least 1% different from each other. If you come up with a reference for the Archaea, please let us know and we can share it with others.
That’s what I thought. Thanks for the help!
Another question regarding chimera detection . . .
Would another possibility be to use chimera.bellerophon or chimera.pintail with the SILVA SEED databases I used to align?
It sounds like neither option would be as good as chimera.slayer, but I don’t have the knowledge to come up with an archaea.gold alignment. Would they be a second choice?
Thanks again!
Frankly, I’d stay away from Bellerophon at this point. The alternative to the gold database that I’d suggest is to use the SILVA-alignments.
Heia,
I am also looking for a ‘gold’ alignment that contains both archaea and bacteria. Any news about where I can get one?
Camilla