My aim is to characterize plant viral genome from nanopore reads. I am doing reference based assembly. First mapping the reads to the reference genome with minimap2 and polishing with nanopolish. In nanopolish variants, the reference file which I have to use contains 3 contigs
> contig1 ATGC > contig2 ATGCA > contig3 ATGCAT
From what I understood, I can do
nanopolish variants -r reads.fasta -b reads.sorted.bam -g draft.fa -w "contig1:0-4" -o polished.vcf
If it is larger genome nanopolish_makerange.py can be used to split. By default it is splitting a single contig into 50kb of segments. But my reference file is a viral genome which has approx 1kb of 3 contigs
If I want to to call variants for all three contig in parallel and to result in polished.vcf for all three contigs how to change the parameters?
Help please. Thank you.