I am new to doing metagenomic studies. My co-adviser introduced me to KBase for analysis and I followed the tutorial narrative protocol on " Genome Extraction from Shotgun Metagenome Sequence Data."
What I've only done was just pair the reads, remove the adapters and low-quality reads. After which, I had them run on Kaiju for taxonomic classification with resolution down to species level. I've read some journals doing annotation without assembly, but I have not read doing the same thing with 16S data.
I may have overlooked that the platform mainly supports shotgun metagenomics. I'm not confident and will plan to do a common pipeline such as the MiSeqSOP by Mothur. But are my results valid, even with low confidence/accuracy?