How to correctly add Source Modifiers for genbank submisson?

[ammaraziz]

Hi,

Thanks for creating and maintaining this very useful program.

I am trying to include patient metadata for the NCBI submission part of the process. Similar to gisaid which allows gender, passage etc, NCBI allows source modifiers such as sex.

I am not 100% sure how to include such information for the NCBI part of the metadata in the config file.

genbank_src_metadata:
  column_names:
    isolate: genbank_name
    host: host
    country: location
    isolation-source: isolation_source

Lets say I wanted to include the ncbi source modifier Sex (assuming I have a column in my metadata called gender), would I add the following:

genbank_src_metadata:
  column_names:
  ....
  Sex: gender

Is that correct?

A related question, for the structured data section eg:

COMMENT     ##Assembly-Data-START##
            Assembly Method       :: CLC Genomics
            Sequencing Technology :: PacBio Sequel II
            ##Assembly-Data-END##

How can I add more information than?

My main aim is to match all the metadata that is required in gisaid to ncbi submission.

Thanks,

Ammar

[dthoward96]

That is correct. You can add as many extra columns to those fields in the config file as you have available. It works the same way for editing the structured comment file. You just need to make sure you add the correct field names that match your data's header to the structured comment section of the config file. For available fields for the structured comment this provides some of that information: https://www.ncbi.nlm.nih.gov/genbank/structuredcomment/