New method to get seqs from Genbase

[xz-keg]

It seems that Genbase updates recently and https://ngdc.cncb.ac.cn/ncov/genome/search now has a delay and no longer displays all seqs.

However, according to @Walde1nsamkeit, we can get seqs from https://download2.cncb.ac.cn/genbase/daily/ and choose the daily updated fas_nt file which is the most recent.

[AngieHinrichs]

Thanks for the info. Do you have any more info about "no longer displays all seqs" -- is there a category of sequences that are excluded?

I see there are sequences for other organisms besides SARS-CoV-2 (e.g. https://download2.cncb.ac.cn/genbase/daily/20250609.fsa_nt.gz), and the metadata would need to be parsed out of GenBank flat files, but that is straightforward. My process that uses the API doesn't yet have the IDs in the 20250610 files, but that could be because it ran about 14 hours ago (shortly after midnight in the Pacific time zone) and the 20250610 files are newer than that. I have had some troubles with the API in the past, and if it seems to shut down again then I can try the files.

[xz-keg]

Thanks for the info. Do you have any more info about "no longer displays all seqs" -- is there a category of sequences that are excluded?

It now has around a week's delay compared to the direct download.

[AngieHinrichs]

The most recent file before 20250610 that contains SARS-CoV-2 sequences is 20250606, which is ~3 days before my automated job ran this morning. I checked a couple IDs from that file (C_AA109982.1, C_AA109997.1) and they first appeared in my API-downloaded set on 2025-06-08 (shortly after midnight Pacific time). There's a day's delay because of time zones and build schedule, so it looks like one extra day of delay in addition to that.

[xz-keg]

The most recent file before 20250610 that contains SARS-CoV-2 sequences is 20250606, which is ~3 days before my automated job ran this morning. I checked a couple IDs from that file (C_AA109982.1, C_AA109997.1) and they first appeared in my API-downloaded set on 2025-06-08 (shortly after midnight Pacific time). There's a day's delay because of time zones and build schedule, so it looks like one extra day of delay in addition to that.

yeah but 20250527 appears on the API first at 6-4. Sometimes the delay can be as long as 1 week.