Q(uestion): For projects submitted to GOLD by external users, do we need to submit our sequences to NCBI first to get the NCBI umbrella Name/ID? Or can it remain an empty field?
A(nswer): No you do not need to submit your sequences to NCBI before submitting project metadata in GOLD. To reiterate what Reddy said earlier, NCBI Umbrella BioProject only applies to large scale studies with several projects under them. example Human Microbiome Project
Q: How do you determine the sequencing quality of your project?
A: You can find more information in our help section under GOLD Terminology and in this publication.
Q: Do the external references come from NCBI?
A: On a GOLD AP external references such as GenBank ID, Assembly Accession, Release date and SRA Runs come from NCBI. Once your genome is annotated in IMG, the IMG Taxon ID will show up in the external references section of the AP.
Q: How long does the entire submission process usually take?
A: That depends on whether it’s an isolate or a metagenome. Isolates generally get processed within 2 weeks; metagenome loading depends on the current IMG workload. They may show up within the same 2 weeks or take a lot longer if we have to process a large batch of JGI-generated data, which takes priority.
Q: Can we get a copy of Marcel’s slides too?
A: They were emailed to you – they’re all in a single pdf and should follow GOLD slides.
Q: If you have a study where you want to annotate genomes of several isolates, do you need to submit individual sequencing projects for each individually?
A: For large submissions, email GOLD and IMG teams.