Test more SARS-CoV-2 samples
@dmacmillan is already working on this.
Since Apr 22, 2020.
- Dominant language
- Python
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Description
After finishing the SARS-CoV-2 support in #549, do more extensive testing with published sample data. List of samples to download and the toolkit to download with.
Find more samples from SRA by searching for "Severe acute respiratory syndrome-related coronavirus"[orgn:__txid694009]. You can filter by platform, and there are currently 466 Illumina records.
It can be tricky to find the published consensus sequences for a sample. I registered for GISAID and found Accession EPI_ISL_408670, but it took me a while to figure out that the descriptions in the SRA abstract for SRR11140746 (SARS-CoV-2/2019-nCoV/USA-WI-1/2020) loosely match the virus name in GISAID for EPI_ISL_408670 (hCoV-19/USA/WI1/2020).
Art's advice:
I queried the SRR number in the NCBI SRA database to get the sample description and then searched for a similar description in the GISAID annotations. Not perfect, I know.
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