Following commands can be used as a guide. Note, paramater selection depends on your hypothesis.
minimap2 -ax map-ont -L -t 8 human-ref.mmi swedish_genome.fastq | samtools sort -@8 -o swedish_genome.bam
minimap2 -ax map-pb -L -t 8 human-ref.mmi swedish_genome.fastq | samtools sort -@8 -o swedish_genome.bam
qualimap bamqc -bam swedish_genome.bam -nw 400 -hm 3
sambamba view -h -t 10 -s 0.5 -f bam --subsampling-seed=16 file.bam -o subsampled_file.bam
Following will extract variants of >=50bp length
sniffles --report_seq --report_BND -l 50 --genotype --mapped_reads file.bam --vcf output_file.vcf 2> sniffles_run.log