Nanopolish makerange for smaller contigs
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2.6 years ago
SUDOsundu ▴ 60

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

For example

    > 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?

assembly genome • 735 views