Description of the data sets used for aligner comparisons.

The Illumina and PacBio data for A. thaliana is available from [23]; the human Illumina and PacBio reads are from the Ashkenazi child data set (available from the Genome in a Bottle project [24], NCBI SRA accession SRX847862). The reference genomes are the Arabidopsis thaliana Col-0 reference genome [18], the human reference genome version GRCh38.p7 [19], and the chimpanzee (Pan troglodytes) genome [20] (release PanTro4, GenBank accession GCF00001515.6).