Chr 21 pangenome experiment. The subfigures compare different performance metrics across all aligners. Marker color indicates the aligner, and marker shape indicates the number of haplotypes in the pangenome reference. (A) CPU time and peak memory usage for building the Chr 21 pangenome indexes for all aligners, excluding GraphAligner owing to its lack of an in-built indexing method. (B) CPU alignment times. (C) Peak memory usage during alignments. (D) Precision and recall of the alignments, excluding the pangenome alignments of Bowtie 2, BWA, and minimap2 owing to their lack of liftover functionality. Most markers are within the red rectangle. (E) Precision and recall of alignments located within the red rectangle in D. (F) The mapping quality curves of the alignments produced by the pangenome aligners to the 500-haplotype Chr 21 pangenome.
