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Protocol for genome assembly of Sars-cov-2 sequences

Do you have a protocol using open source software for assembling SARS-CoV-2 genome sequences after Ampliseq sequencing?

sars sars-cov-2 genome assembly
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updated by GenoMax GenoMax • written by fhsantanna fhsantanna

You should be able to use SPAdes or even tadpole.sh from BBMap suite for the assembly. Method/tools used by the Nextstrain project should be useful to find relationships once you have the sequences assembled.

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written by GenoMax GenoMax

Spades is for de novo assembly, isn't it? Wouldn't a reference based assembly method be faster?

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written by fhsantanna fhsantanna

Since this is a simple (relatively) genome a de novo assembly should work. Doing simple alignments would get you much faster results if you are ok with using the reference genome available.

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written by GenoMax GenoMax

is this the ampliseq panel for SARS-CoV-2 ? they have Trinity setup as a torrent suite plug-in that you can use within the software that they provide.

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written by Kevin Kevin

Yes, Kevin. It is the ampliseq panel for SARS-CoV-2. Could you please give me more details about it? I have inquired the technical support the same question, but they responded that we would have to use basespace.

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written by fhsantanna fhsantanna

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