Readmapping - long reads
Indexing
When provided with a reference genome, LightSpeed first generates a Burrows-Wheeler based index of all the sequences. After the first run, the index is cached and reused on later runs.
Read mapping
LightSpeed Long Reads to Germline Variants aligns long reads to a reference using minimap2 [Li, 2018], but has been optimized for increased speed.
When mapping Oxford Nanopore reads, the settings in the minimap2 preset "lr:hq" is used.
When mapping PacBio HiFi reads, the settings in the minimap2 preset "map-hifi" is used.