Protocol for genome assembly of Sars-cov-2 sequences

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4.4 years ago

fhsantanna ▴ 620

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 • 1.8k views

ADD COMMENT • link updated 4.4 years ago by GenoMax 147k • written 4.4 years ago by fhsantanna ▴ 620

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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.

ADD REPLY • link 4.4 years ago by GenoMax 147k

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

ADD REPLY • link 4.4 years ago by fhsantanna ▴ 620

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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.

ADD REPLY • link 4.4 years ago by GenoMax 147k

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Check the SARS-CoV-2 analysis pipeline by ARTIC consortium.

https://github.com/nf-core/viralrecon

ADD REPLY • link 4.4 years ago by Arup Ghosh 3.2k

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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.

ADD REPLY • link 4.4 years ago by Kevin ▴ 640

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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.

ADD REPLY • link 4.4 years ago by fhsantanna ▴ 620

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