Getting data and metadata

animesh-workplace / sars-frontend

INSACOG DataHub is a part of INSACOG that is used to store and analyze SARS-CoV-2 genomic data. This repository is developed and maintained at National Institute of Biomedical Genomics.

https://research.nibmg.ac.in/insacog/

GNU General Public License v3.0

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Getting data and metadata #3

Closed saketkc closed 2 years ago

saketkc commented 2 years ago

Hi,

Thanks for creating and maintaining this great interface! Is it possible to include a flatfile(csv/tsv) dump of all the sequences being deposited which at the bare minimum as the following fields:

1. ID
2. Pangolin lineage
3. Age
4. Gender
5. Variant
3. State
4. District
5. City/Location
6. Submitting lab
7. Originating Lab
8. Collection Date
9. Submission Date
10. Sequencing Platform
11. QC metrics for fasta sequences
12. Any other clinically relevant metadata (this in my opinion currently does not exist, but would be extremely useful)

Thanks! Saket

animesh-workplace commented 2 years ago

Most of the information requested is also available on GISAID, but if you still need access to this data you can apply to INSACOG consortium @saketkc

saketkc commented 2 years ago

Thanks, I am aware and have been using data from GISAID. Can you help me with the link for raising a request for data access to INSACOG? My understanding is that only participating laboratories only have access - are individuals allowed to access the data through some sort of membership?

animesh-workplace commented 2 years ago

This resource from DBT INSACOG website might be helpful. Extremely sorry for the delay in response

saketkc commented 2 years ago

No worries, thanks! I understand.