Table 2.

An overview of software tools for analysing long-read sequencing data

Category	Tool name	Description	Ref.
De novo assembly	(Hi)Canu	Versatile de novo assembler	23
	Flye	Fast de novo assembler that can also operate on low coverage data	24
	Shasta	Fast ONT assembler	25
	Falcon Unzip	PacBio assembler for phased assemblies	22
	Peregrine	Optimized assembler for HiFi data only	128
	hifiasm	Optimized assembler for HiFi data only	139
	PGAS	Phased assembly including strand seq	46
Genomic alignment	LAST	Versatile method to align contigs or genomes	57
	MUMmer	Long-standing genomic aligner	87
	minimap2	Pairwise alignment method for long reads up to genomes	58
	Cactus	Progressive genomic alignment method allowing integration of more than two genomes at a time	90
	SibeliaZ	Fast genome aligner of multiple genomes	140
Read alignment	minimap2	Pairwise alignment method for long reads up to genomes	58
	NGMLR	Convex gap cost implementation	42
	Winnowmap	Improvements for mapping in repetitive regions	59
	lra	Efficient convex-cost gap penalty sequence and contig aligner	60
Graph genome methods	Giraffe	Rapid reads to graph aligner	45
	vg	Toolkit to construct and convert graphs with methods to genotype and call variants	96
	minigraph	A sequence-to-graph mapper and graph constructor based on minimap2	97
	GraphAligner	Sequence-to-graph aligner for long reads	141
	GraphTyper2	Genotyping variants in a graph genome from short reads	100
	Paragraph	Genotyping structural variants in a regional graph genome from short reads	101
	PanGenie	k-mer-based genotyping of short reads in a haplotype-resolved graph	99
Phasing	WhatsHap	Phasing method for SNVs and smaller indels	15
	HapCut2	Phasing method for SNVs	16
SV calling from alignment	pbsv	Joint calling of SVs across samples	62
	Sniffles	Automatic parameter estimation	42
	CuteSV	Highly parallelized SV calling	63
	SVIM	Uses graph-based clustering of candidates	61
SV calling from assemblies	dipcall	Deletion and insertion calling from de novo assembly	89
	SVIM-asm	SV calling from (diploid) de novo assembly	142
	PAV	Compares phased assemblies with a reference genome	46
SNV calling	Clair	Uses a convolutional neural net	69
	DeepVariant	Neural network-based SNV caller	67
	Longshot	Partitioning reads in haplotypes and calling variants in accordance with those haplotypes	70
	Pepper	Phasing-based SNV calling	68
SV merging	SURVIVOR	Merging that allows breakpoint inaccuracies	113
	SVanalyzer	Assembly based, two samples only	98
	Truvari	Parameterized stepwise merging including sequence similarity	9
	Jasmine	Merging SV based on sequence similarity	32
SV genotyping	cuteSV	Force-calling of variants from a VCF file	63
	Sniffles	Uses split reads to identify known SVs over shared breakpoints	42
	SVJedi	Compares the alignment of reads against the reference genome and alternative contigs representing the SV to determine the best match	66
	LRcaller	Genotypes variants of long reads	11
Other	TRiCoLOR	Detects and genotypes repeat lengths separated by phase	76
	Iris	Local assembly of insertions	32
	SVCollector	Optimized sample selection	43
	NanoComp	Comparison of sequencing data	53

HiFi, high fidelity; indel, insertions–deletions; ONT, Oxford Nanopore Technologies; PacBio, Pacific Biosciences; SNV, single-nucleotide variant; SV, structural variant; VCF, variant call format.