I’m planning on using the silva database for my metagenomic analysis and was hoping to get a few things clarified -
The silva.bacteria.fasta currently available in the MiSeq SOP was compiled using which version of the silva database? Also apart from this, where can I get the .fasta files for the database?
The silva v132 full length database downloaded from https://mothur.org/wiki/silva_reference_files/, has only a .align file and a .tax file. Can I use the .align file instead of the fasta file for customizing the database using pcr.seqs and use that output in the “reference=” parameter instead of the fasta file as instructed in the MiSeq SOP?
I would like someone to verify if my understanding is correct - the full length database available in the above link is basically the silva full database aligned using a few sequences that are available under the SEED database. What is the purpose of doing do? And, if I were to use these 2 databases for aligning a query sequence how would I go about doing the same?
Thanks in advance for all the help.
EDIT: Additionally I want to know why in MiSeq SOP, the alignment is done with Silva, while the Bayesian classifier is done with RDP. Is there any dis-advantage of using Silva itself?