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. The tool provides a primary read alignment that is directly visible in the reads track output. In addition, supplementary alignments are generated. Information about supplementary alignments is embedded in the reads track, but is not directly accessible. When the reads track is used as input to Structural Variant Caller for Long Reads, the supplementary alignments are used for identification of structural variants.
When mapping Oxford Nanopore reads, the settings in the minimap2 preset "lr:hq" are used.
When mapping PacBio HiFi reads, the settings in the minimap2 preset "map-hifi" are used.