Table 2.

Evaluated aligners and SV callers

Name	Type	Version	Release year	Threads	Language	Description	Citation
GraphMap	Aligner	0.5.2	2016	16	C++	Aligns nanopore long reads with circular genome handling	[19]
LAST	Aligner	941	2011	16	C++	Modified BLAST, outputs MAF format	[20]
minimap2	Aligner	2.1	2017	16	C	Aligns error-prone long reads, faster and more accurate than BWA	[21]
NGMLR	Aligner	0.2.6	2017	16	C++	Works with nanopore long reads to generate high-quality SV calls	[22]
NanoSV	SV caller	1.2.0	2017	16	Python	Identifies and clusters split reads based on genomic positions and orientations to identify breakpoint junctions of SVs	[23]
Picky	SV caller	0.2.a	2017	16	Perl	“Pick”-and-stitch segments from LAST alignments into representative alignments with a greedy algorithm	[24]
Sniffles	SV caller	1.0.8	2017	16	C++	Detects all types of SVs using split-read alignments, high-mismatch regions, and depth of coverage	[22]