#!/bin/sh

PATH=.:$PATH

# long sequences against a reference genome
minimap2 -a test/MT-human.fa test/MT-orang.fa > test.sam
# create an index first and then map
minimap2 -d MT-human.mmi test/MT-human.fa
minimap2 -a MT-human.mmi test/MT-orang.fa > test.sam
# # use presets (no test data)
# minimap2 -ax map-pb ref.fa pacbio.fq.gz > aln.sam       # PacBio genomic reads
# minimap2 -ax map-ont ref.fa ont.fq.gz > aln.sam         # Oxford Nanopore genomic reads
# minimap2 -ax sr ref.fa read1.fa read2.fa > aln.sam      # short genomic paired-end reads
# minimap2 -ax splice ref.fa rna-reads.fa > aln.sam       # spliced long reads (strand unknown)
# minimap2 -ax splice -uf -k14 ref.fa reads.fa > aln.sam  # noisy Nanopore Direct RNA-seq
# minimap2 -ax splice -uf -C5 ref.fa query.fa > aln.sam   # Final PacBio Iso-seq or traditional cDNA
# minimap2 -cx asm5 asm1.fa asm2.fa > aln.paf             # intra-species asm-to-asm alignment
# minimap2 -x ava-pb reads.fa reads.fa > overlaps.paf     # PacBio read overlap
# minimap2 -x ava-ont reads.fa reads.fa > overlaps.paf    # Nanopore read overlap
