"I have used Nephele for analysis and am ready to publish a manuscript. I first need to submit my sequencing files to National Center for Biotechnology Information (NCBI)'s Sequence Read Archive (SRA). Is there an easy way to do that?"
Yes! – go to METAGENOTE (https://metagenote.niaid.nih.gov) and use the Nephele's metadata file to complete your annotation and submission directly from METAGENOTE.
Please watch this video on how to submit your data to SRA.