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?

Help please. Thank you.

assembly genome • 735 views
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