Table 1.

Evaluation of junction accuracy on 2D ONT reads

	GMAP	minimap2	SpAln	STAR
Run time (CPU min)	631	15.9	2076	33.9
Peak RAM (GByte)	8.9	14.5	3.2	29.2
# aligned reads	103 669	104 199	103 711	26 479
# chimeric alignments	1904	1488	0	0
# non-spliced alignments	15 854	14 798	17 033	10 545
# aligned introns	692 275	693 553	692 945	78 603
# novel introns	11 239	3113	8550	1214
% exact introns	83.8	94.0	87.9	55.2
% approx. introns	91.8	96.9	92.5	82.4

Notes: Mouse cDNA reads (AC: SRR5286960; R9.4 chemistry) were mapped to the primary assembly of mouse genome GRCm38 with the following tools and command options: minimap2 (‘-ax splice’); GMAP (‘-n 0 –min-intronlength 30 –cross-species’); SpAln (‘-Q7 -LS -S3’); STARlong (according to http://bit.ly/star-pb). The alignments were compared to the EnsEMBL gene annotation, release 89. A predicted intron is novel if it has no overlaps with any annotated introns. An intron is exact if it is identical to an annotated intron. An intron is approximate if both its 5′- and 3′-end are within 10 bp around the ends of an annotated intron. Chimeric alignments are defined in the SAM spec (Li et al., 2009).