So the problem is stated in the title. The two genomes are from NCBI (SARS-CoV-2). In addition, I want to obtain the variants. I want to note that the sequences are highly similar, and I think the task should be facilitated by this similarity
I almost finished my script using biopython but a run_out_of_Memory-error appeard after I switched from my 20 bp toy-sequence to the 30kb genome. I found then that biopython is more a tool to glue other programs together.
I tried using mafft, and it runs, but I get a weird error. (ApplicationError: Non-zero return code 1 from 'mafft Ref_andOneMore.fasta', message 'nthread = 0' ) I'm further trying MAFFT, but I doubt that this is the right tool. Can somebody tell me what pipeline is best suited for this task?
Why do you voluntarily make things harder by using these tools through python? Can you not just use MAFFT or any other tool directly?