Uploading Metadata and Creating SRA Submission Using mixS Package for Metagenomic samples Within NCBI Submission Portal v1

PURPOSE: This document provides detailed instructions on how to submit metagenomic sequences (targeted and shotgun) data and associated contextual data to NCBI, while adhering to the INSDC standard data structure, "Pathogen DOM,". https://genomicsstandardsconsortium.github.io/mixs/. The protocol includes essential steps to create a new NCBI submission environment for your laboratory group, using MixS metadata package which is crucial to have in place before data are submitted. After these initial setups, the the remaining protocol focuses on step-by-step instructions for data submission. SCOPE: This protocol is intended for any laboratory submitting metagenomic data from any food, farm, environmental samples using MixS metadata package to NCBI. GUIDANCE FOR NEW SUBMITTERS: Before initiating your first data submission, there is significant preparatory work required. We advise designating a team member to spend several days setting up the necessary systems well before your anticipated first submission. Watch NCBI's 10min video tutorial describing general submission of whole genome sequences (WGS) to SRA. ADVICE FOR FREQUENT/LARGE VOLUME SUBMISSIONS: Start by following Step 1 to establish your NCBI submission environment. For ongoing or large-scale submissions, email gb-admin@ncbi.nlm.nih.gov to arrange an account for API-based submissions.