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EBI-Metagenomics / genome_uploader

Python script to upload bins and MAGs to ENA (European Nucleotide Archive)
Apache License 2.0
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Co-assembly of the same sample #5

Closed SilasK closed 1 year ago

SilasK commented 1 year ago

The is more a question of interpretation.

The script shows an error if there are multiple runs listed but co-assembly=FALSE. I understand that this is criteria is checked. but in my case I used all the runs of the same bioSample. To my understanding this is not co-assembly.

Ge94 commented 1 year ago

Hi Silas, I acknowledge this sounds confusing. The official definition of co-assembly is that it is an assembly generated from raw reads from different files, regardless of them being technical replicates of the same sample or not. The case you are focusing on is actually ideal for generating co-assemblies, as they allow to exploit low-abundant species that might not come up by assembling a single run, but only by including multiple replicates of the same sample. In any case, if more than one run was used to generate an assembly, then it needs to be labelled as co-assembly according to ENA.