Software tools that use genome-guided alignment include Bowtie,[56] TopHat (which builds on BowTie results to align splice junctions),[57][58] Subread,[59] STAR,[55] HISAT2,[60] Sailfish,[61] Kallisto,[62] and GMAP.[63] The quality of a genome guided assembly can be measured with both 1) de novo assembly metrics (e.g., N50) and 2) comparisons to known transcript, splice junction, genome, and protein sequences using precision, recall, or their combination (e.g., F1 score).[10] In addition, in silico assessment could be performed using simulated reads.[64][65]