Hi all, appreciate the pipeline is still under development, but am curious if it is currently usable? I have ~1.5k MAGs/binned metagenomes + 90 primary metagenome assemblies to submit, and am looking for anything that will make that easier 😅

Hi! I think you can try to run from dev brunch already. We have a user that uploaded data successfully yesterday 💫

Thanks, I will give it a try 🎉 I am currently in the process of uploading ~12Tb of raw read data, so it might wait a week or two 🫣 Can you pass a list of multiple run accessions for the metagenome assemblies? I have co-assemblies assembled from multiple runs.

good question! our uploading tool itself supports co-assemblies but I guess we need to modify seqsubmit schema a bit for it. I will add it to urgent TODO to resolve before you finish with your reads upload

That would be amazing, thanks!

I have a following questions 1. do you have coverage calculated for your co-assemblies already? 2. you will need to create an umbrella sample for co-assemblies. Do you know how to do it?

1. do you have coverage calculated for your co-assemblies already?

Technically no, I made these a number of years ago and don't have the data/facility to re-calculate this. I was going to fudge a number 🫣

1. you will need to create an umbrella sample for co-assemblies. Do you know how to do it?

That I don't - it's not enough to just create a sample for the co-assembly that references all the run accessions?

Basically yes. You need a sample that references all samples used in a co assembly. A bit explanation you can find in this little pdf

Ah, that looks reasonably simple

about coverage. Pipeline can calculate coverage if you will specify fastq files as input. But for co-assemblies it would be computationally difficult but possible. So, in that case if you can provide coverage magic numbers it will be better for everyone 😁

Most of our Tree of Life metagenomes until quite recently all got given an arbitrary value of 31 for coverage 🫢🫢🫢

good to know!😆