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AIRR Community Common Repository Working Group
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Recommendation 5: Location of processed repertoire-sequencing data #7

Closed bussec closed 7 years ago

bussec commented 7 years ago

The data referred to in recommendation 5 is a superset of the data defined in the current minimal standards WG (MiniStd) draft, sections 5, 6 and 7 (information on processing, processed sequences, basic V(D)J+CDR3 annotation). However, currently MiniStd assumes that the information of sections 5-7 will be stored in Genbank or TSA and is trying to map the respective fields of sections 5-7 to the INSDC Feature Table. The main consideration behind this is that until the distributed AIRR repository infrastructure described by this document is accepted for data deposition by journals and funders, MiniStd has to recommend suitable procedures for deposition of essential data in generic (non-AIRR) repositories.

This issue will likely resolve in time, but for now there should be consistent solution between the MiniStd and the Common Repo recommendations.

bussec commented 7 years ago

Please note: The Recommendation that this issue refers to has been re-number to #6 as of 2016-11-17.

bussec commented 7 years ago

The minimal standards (MiniStd) group has elaborated this issue further over the last weeks. The current status is that MiniStd section 6 (consensus sequence) & 7 (VDJ segment inferrence) information will be deposited at Genbank. We have been in contact with both NCBI and EBI, and there are no blockers from the repository side that would prevent this way of deposition. This recommendation should be changed to reflect this.

bussec commented 7 years ago

Resolved in commit 724ee19.