Do you have a protocol using open source software for assembling SARS-CoV-2 genome sequences after Ampliseq sequencing?
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.
Spades is for de novo assembly, isn't it? Wouldn't a reference based assembly method be faster?
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.
Check the SARS-CoV-2 analysis pipeline by ARTIC consortium.
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.
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.