TABLE 1.

Tools specifically developed to handle the alignment and structural variant calling on nanopore data.

Tool	Description	Input	Algorithm	Link	Reference
GraphMap	Aligner	FASTA/FASTQ	Global alignment	https://github.com/isovic/graphmap	Sović et al. (2016)
BWA	Aligner	FASTA/FASTQ	BWA-SW	https://github.com/lh3/bwa	H. Li and Durbin (2010)
minimap2	Aligner	FASTA/FASTQ	Seed-chain-align	https://github.com/lh3/minimap2	H. Li (2018)
NGMLR	Aligner	FASTA/FASTQ	Convex scoring model	https://github.com/philres/ngmlr	Sedlazeck et al. (2018)
LAST	Aligner	FASTA/FASTQ	Adaptive seed	https://github.com/mcfrith/last-genome-alignments	Kiełbasa et al. (2011)
LAMSA	Aligner	FASTA/FASTQ	SDP-based algorithm	https://github.com/yangao07/LAMSA	Liu et al. (2017)
LRA	Aligner	FASTA/FASTQ	Heuristic finding approximate local alignment	https://github.com/ChaissonLab/LRA	Ren and Chaisson (2021)
Sniffles	SV-caller	BAM	Putative variant scoring. Variant scoring and genotyping. Clustering and nested SVs	https://github.com/fritzsedlazeck/Sniffles	Sedlaeck et al. (2018)
Sniffles2	SV-caller	BAM	Three-phase clustering process	https://github.com/fritzsedlazeck/Sniffles	Sedlazeck et al. (2018), Smolka et al. (2022)
SVIM	SV-caller	FASTQ/BAM	Collection of SV signatures. Clustering of the SV signatures. Combination and classification of the signatures	https://github.com/eldariont/svim	Heller and Vingron (2021)
NanoVar	SV-caller	BAM	Artificial neural network model	https://github.com/benoukraflab/NanoVar	Tham et al. (2020)
NanoSV	SV-caller	BAM	Clustering of split reads to identify SV breakpoint junctions	https://github.com/mroosmalen/nanosv	Cretu Stancu et al. (2017)
cuteSV	SV-caller	BAM	Heuristic method	https://github.com/tjiangHIT/cuteSV	Jiang et al. (2020)
Nano-GLADIATOR	CNV-caller	BAM	Read count	https://sourceforge.net/projects/nanogladiator/	Magi et al. (2019)
QDNAseq	CNV-caller	BAM	Read count	https://github.com/ccagc/QDNAseq	Scheinin et al. (2014)