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#generic mapping reads minimap2 -a ref.fa ont-reads.fq > aln.sam #mapping noisy reads minimap2 -ax map-ont ref.fa ont-reads.fq > aln.sam # for Oxford Nanopore reads |
Full genome/assembly alignment
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minimap2 -ax asm5 ref.fa asm.fa > aln.sam # assembly to assembly/ref alignment |
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