Short RNA-seq read alignment with minimap2

TL;DR: the new preset splice:sr in minimap2 can align short RNA-seq reads. It is similar to STAR in resource usage, approaches STAR in junction accuracy, and is overall better at SNP calling. Minimap2 can align short or long genomic reads and long RNA-seq reads. Short RNA-seq read alignment is a notable omission. This is changed with the latest v2.29 release — minimap2 now has a new splice:sr…