minimap2

Versatile pairwise aligner for genomic and spliced nucleotide sequences

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Versatile pairwise aligner for genomic and spliced nucleotide sequences

minimap2

Align long reads to a reference genome$ minimap2 -a reference.fasta reads.fastq > alignments.sam

Map spliced reads (RNA-seq) to genome with preset$ minimap2 -ax splice reference.fasta rna_reads.fastq > output.sam

Perform all-vs-all alignment for sequence comparison$ minimap2 -x ava-ont sequences.fasta sequences.fasta > overlaps.paf