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SARS-CoV2 strain identifying strain

Hello,

I have a few contigs that turned out to be SARS-CoV2 from a sample, how can I identify the strain? what tools I can use for this?

Thanks

covid19 sars-cov-2 gisaid
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updated by Ram Ram • written by eli_bayat • eli_bayat

2 answers

You can try pangolin (LINK). Use the web front-end if you have only a few things to screen.

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written by GenoMax GenoMax

Thank you so much for your suggestion. I have 4 sequences, and I used the link you sent me. 3 of them failed the analysis and 1 of them gave B.1 lineage. Does this mean one of them the strain is B.1 and there is no identified strain for the others?

Thanks in advance for the help,

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written by eli_bayat • eli_bayat

You may use Nextclade (https://clades.nextstrain.org/), which assigns Nextstrain clades to the sequences.

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written by raunakms raunakms

This is really nice, thank you so much. When I uploaded my sequences, out of 4, only 2 of them were successful and showed the clades. Does this mean, the other two does not have known strain or something?

Thank you for the help

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written by eli_bayat • eli_bayat

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