Question: Protocol for genome assembly of Sars-cov-2 sequences
0
gravatar for fhsantanna
4 weeks ago by
fhsantanna490
Brazil
fhsantanna490 wrote:

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

assembly sars-cov-2 genome sars • 114 views
ADD COMMENTlink modified 4 weeks ago by genomax87k • written 4 weeks ago by fhsantanna490
1

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 REPLYlink modified 4 weeks ago • written 4 weeks ago by genomax87k

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

ADD REPLYlink written 28 days ago by fhsantanna490
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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 REPLYlink written 28 days ago by genomax87k
1

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

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

ADD REPLYlink written 4 weeks ago by Arup Ghosh2.6k
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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 REPLYlink written 29 days ago by Kevin640

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 REPLYlink written 28 days ago by fhsantanna490
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