Source of short read sequences
DDBJ Sequence Read Archive (DRA)
Classification of metagenomes by sampling environments
Current classification of metagenome in NCBI taxonomy
NCBI taxonomy
Other 16S rRNA databases (ordered by alphabet)
Greengenes
The Ribosomal Database Project (RDP)
SILVA
'The All-Species Living Tree' Project in SILVA
Tools
NGS QC Toolkit: For quality control of NGS data
SortMeRNA: For predicting ribosomal RNA sequences from NGS data
Source of 16S rRNA sequences for using SortMeRNA: Silva release 115 SSU Ref NR99 (FASTA file compressed by gzip)
UCHIME: For detecting chimeric sequences
CD-HIT: For clustering a set of sequences
CD-HIT-454: For removing duplicates generated by Roche 454 platform
RDP Classifier: For assigning taxonomy to 16S rRNA sequences (Source code)
NCBI BLAST: For searching regions with similarity between sequences
stand-alone BLAST applications: For using BLAST in your own systems