The SARS-CoV-2 genome alignment option

Question

[natasha.sernova]

Dear all, Nowadays many scientists have to solve some problems related to SARS-CoV-2. The viral genomes are huge(~30kb). Is it correct, that to align several of them I have to put those fasta-genomes to a single file, add a reference genome to the same file and run a proper tool like MAFFT?

(like here - https://www.biostars.org/p/187360/) It will be my next question – what MAFFT-option I should use? Probably MAFFT-L-INS-i, since «More specifically, in Figure 1 in Le et al. [18], the advantage of MAFFT-L-INS-i (an iterative refinement method) over MAFFT-L-INS-1 (a progressive method) was clearly observed for a small number of sequences but not for thousands of sequences.» Thank you! Natalia Sernova

[natasha.sernova]

Unfortunately some genomes are elsewhere, I had to search other dbs to find most of them.

[GenoMax]

You could use the software/procedure nextstrain uses to build their alignments for SARS-CoV-2.

Answer 1

[GenoMax]

Any particular reason you want to do this yourself? NCBI makes genome alignments easy to do via SARS-CoV-2 resource page. Select genomes you want and align. Even build a phylogenetic tree.

You could it all yourself by following plan you described as well.