Minimap2 (available as a plugin in Geneious Prime) is a powerful and versatile sequence alignment program capable of aligning DNA or mRNA sequences against a large reference sequence or sequences. It is particularly useful for mapping long genomic reads (i.e. PacBio and Oxford Nanopore) to whole genomes and can run splice-aware alignment of cDNA or direct RNA reads. Minimap2 can also be used as a fast whole genome alignment tool for genomes with ~15% max divergence by choosing one of your genomes to act as a reference.
In Geneious Prime, minimap2 preset options have been made available which provide the optimal settings for most cases. These presets are available in the "Data Type" dropdown as follows:
map-ont
Align noisy long reads of ~10% error rate to a reference genome. This is the default mode.
lr:hq
Align accurate long reads (error rate <1%) to a reference genome (-k19-w19 -U50,500-g10k). This was recommended by ONT developers for recent Nanopore reads produced with chemistry v14 that can reach ~99% in accuracy. It was shown to work better for accurate Nanopore reads thanmap-hifi.
map-hifi
Align PacBio high-fidelity (HiFi) reads to a reference genome (-xlr:hq-A1 -B4 -O6,26 -E2,1-s200). It differs from lr:hq only in scoring. It has not been tested whether lr:hq would work better for PacBio HiFi reads.
map-pb
Align older PacBio continuous long (CLR) reads to a reference genome (-Hk19). Note that this data type is effectively deprecated by HiFi. Unless you work on very old data, you probably want to use map-hifi or lr:hq.
map-iclr
Align Illumina Complete Long Reads (ICLR) to a reference genome (-k19-B6 -b4-O10,50). This was recommended by Illumina developers.
asm5
Long assembly to reference mapping (-k19-w19 -U50,500 --rmq -r1k,100k -g10k -A1 -B19 -O39,81 -E3,1 -s200 -z200-N50). Typically, the alignment will not extend to regions with 5% or higher sequence divergence. Use this preset if the average divergence is not much higher than 0.1%.
asm10
Long assembly to reference mapping (-k19-w19 -U50,500 --rmq -r1k,100k -g10k -A1 -B9 -O16,41 -E2,1 -s200 -z200-N50). Use this if the average divergence is around 1%.
asm20
Long assembly to reference mapping (-k19-w10 -U50,500 --rmq -r1k,100k -g10k -A1 -B4 -O6,26 -E2,1 -s200 -z200-N50). Use this if the average divergence is around several percent.
splice
Long-read spliced alignment (-k15-w5 --splice -g2k -G200k -A1 -B2 -O2,32 -E1,0 -C9 -z200 -ub --junc-bonus=9 --cap-sw-mem=0--splice-flank=yes). In the splice mode, 1) long deletions are taken as introns and represented as the ‘N’ CIGAR operator; 2) long insertions are disabled; 3) deletion and insertion gap costs are different during chaining; 4) the computation of the ‘ms’ tag ignores introns to demote hits to pseudogenes.
splice:hq
Spliced alignment for accurate long RNA-seq reads such as PacBio iso-seq (-xsplice-C5 -O6,24-B4).
splice:sr
Spliced alignment for short RNA-seq reads (-xsplice:hq--frag=yes --end-bonus=10 -2K50m --heap-sort=yes --pe-ind-chain--secondary=no).
These presets can be modified by selecting "No Preset" and then entering the desired command line options at the bottom of the settings window. Use the above preset options as a guide and change any values as needed. For additional guidance, please see the Minimap2 Manual or Cookbook.