Add EBI sequences and metadata?

[pjotrp]

EBI has some 2K sequences we could bring in too. @AndreaGuarracino can you take a look at:

https://www.covid19dataportal.org/sequences?db=embl

[LLTommy]

EBI and NCBI do sync their data, we should have most (if not all) of those sequences - if they pass the metadata QC. (e.g. https://www.ebi.ac.uk/ena/browser/view/MN996531 and https://www.ncbi.nlm.nih.gov/nuccore/MN996531)

[AndreaGuarracino]

I'm currently working on the sequenced samples:

https://www.ncbi.nlm.nih.gov/sra/?term=txid2697049%5BOrganism%5D

I am almost ready to start the download. I am also parsing the metadata to create a YAML file for each run_accession, so when I am ready to PR the scripts, there will be ontology-decisions to make.

[pjotrp]

Hi @AndreaGuarracino, what is the status of this issue?

[AndreaGuarracino]

Technically, this is an infinite issue.

I periodically update NCBI samples (which are FASTA files), following the guide already published in the blog.

Regarding the EBI samples, to date, I have uploaded 12892 samples downloaded from SRA to the platform, all short-reads ones. The last download session was at the beginning of July, leading to~ 2.4TB of gzipped FASTQ files (both short-reads + long-reads samples). I could download new samples from SRA and push another batch.