Table 1.

List of methods for long-read analysis and its function

FunctionToolTechnologyGitHubCitation
Basecalling (A)CCSPacBiohttps://github.com/PacificBiosciences/ccs
DoradoONThttps://github.com/nanoporetech/dorado
Google Deep ConsensusPacBiohttps://github.com/google/deepconsensusBaid et al. 2023
Reads QC (B)LongReadSumONT/PacBiohttps://github.com/WGLab/LongReadSum
LongQCONT/PacBiohttps://github.com/yfukasawa/LongQCFukasawa et al. 2020
NanoPackONT/PacBiohttps://github.com/wdecoster/nanopackDe Coster et al. 2018
Alignment (C)LRAONT/PacBiohttps://github.com/ChaissonLab/LRARen and Chaisson 2021
minimap2ONT/PacBiohttps://github.com/lh3/minimap2Li 2018, 2021
NGMLRONT/PacBiohttps://github.com/philres/ngmlrSedlazeck et al. 2018b
pbmm2PacBiohttps://github.com/PacificBiosciences/pbmm2
VACmapONT/PacBiohttps://github.com/micahvista/VACmapDing et al. 2024
VulcanONT/PacBiohttps://gitlab.com/treangenlab/vulcanFu et al. 2021
Winnowmap2ONT/PacBiohttps://github.com/marbl/WinnowmapJain et al. 2022
Alignment QC (D)NanoPackONT/PacBiohttps://github.com/wdecoster/nanopackDe Coster et al. 2018
SambambaONT/PacBiohttps://github.com/biod/sambambaTarasov et al. 2015
SAMtoolsONT/PacBiohttps://github.com/samtools/samtoolsLi et al. 2009
SNV & indels calling (E)Clair3ONT/PacBiohttps://github.com/HKU-BAL/Clair3Zheng et al. 2022
DeepSomaticIllumina/ONT/PacBiohttps://github.com/google/deepsomaticPark et al. 2024
DeepVariantONT/PacBiohttps://github.com/google/deepvariantPoplin et al. 2018
LongshotONT/PacBiohttps://github.com/pjedge/longshotEdge and Bansal 2019
SV calling (F)cuteSVONT/PacBiohttps://github.com/tjiangHIT/cuteSVJiang et al. 2020
DELLYONT/PacBio/Illuminahttps://github.com/dellytools/delly?tab=readme-ov-fileRausch et al. 2012
NanomonSVONT/PacBiohttps://github.com/friend1ws/nanomonsvShiraishi et al. 2023
pbsvPacBiohttps://github.com/PacificBiosciences/pbsv
SawfishPacBiohttps://github.com/PacificBiosciences/sawfishSaunders et al. 2024
SeverusONT/PacBiohttps://github.com/KolmogorovLab/SeverusKeskus et al. 2024
Sniffles2ONT/PacBiohttps://github.com/fritzsedlazeck/SnifflesSmolka et al. 2024
SAVANAONT/PacBiohttps://github.com/cortes-ciriano-lab/savanaElrick et al. 2024
SVisionONT/PacBiohttps://github.com/xjtu-omics/SVisionLin et al. 2022b
Copy number variants (G)HiFiCNVPacBiohttps://github.com/PacificBiosciences/HiFiCNV
SpectreONT/PacBiohttps://github.com/fritzsedlazeck/Spectre
Tandem repeat (TRs) (H)MedakaONThttps://github.com/nanoporetech/medakaLee et al. 2021
pathSTRONThttps://github.com/wdecoster/pathSTRDe Coster et al. 2024
StraglrONThttps://github.com/bcgsc/straglrChiu et al. 2021
StrSpyONThttps://github.com/unique379r/strspyHall et al. 2022
TRGTPacBiohttps://github.com/PacificBiosciences/trgtDolzhenko et al. 2024
Genotyping (I)kanpigONT/PacBiohttps://github.com/ACEnglish/kanpigEnglish et al. 2024a
SVJediONT/PacBiohttps://github.com/llecompte/SVJediRomain and Lemaitre 2023
Downstream analysis—phasing (J)HapCUT2ONT/PacBiohttps://github.com/vibansal/HapCUT2Edge et al. 2017
HiPhasePacBiohttps://github.com/PacificBiosciences/HiPhaseHolt et al. 2024
WhatsHapONT/PacBiohttps://github.com/whatshap/whatshapMartin et al. 2023
Downstream analysis—variant annotation (K)AnnotSVNAhttps://github.com/lgmgeo/AnnotSVGeoffroy et al. 2018
ANNOVARNAhttp://annovar.openbioinformatics.org/Wang et al. 2010
CADDNAhttps://cadd.gs.washington.edu/Kircher et al. 2014
CADD-SVNAhttps://github.com/kircherlab/CADD-SVKleinert and Kircher 2022
DANNNAhttps://cbcl.ics.uci.edu/public_data/DANN/Quang et al. 2015
PolyPhen-2NAhttp://genetics.bwh.harvard.edu/pph2/Adzhubei et al. 2013
SIFTNAhttps://sift.bii.a-star.edu.sg/Sim et al. 2012
SnpEffNAhttps://pcingola.github.io/SnpEff/Cingolani et al. 2012
SvAnnaONT/PacBiohttps://github.com/monarch-initiative/SvAnnaDanis et al. 2022
SVAFotateNAhttps://github.com/fakedrtom/SVAFotateNicholas et al. 2022
VEPNAhttps://github.com/Ensembl/ensembl-vepHunt et al. 2022
Downstream analysis—methylation calling (L)DoradoONThttps://github.com/nanoporetech/dorado
fibertools-rs/ftPacBiohttps://github.com/fiberseq/fibertools-rsJha et al. 2024
JasminePacBiohttps://github.com/PacificBiosciences/jasmine
ModkitONThttps://github.com/nanoporetech/modkit
Assembly (M)CanuONT/PacBiohttps://github.com/marbl/canuKoren et al. 2017
FlyeONThttps://github.com/mikolmogorov/FlyeKonings et al. 2024
hifiasmONT/PacBiohttps://github.com/chhylp123/hifiasmCheng et al. 2021
ShastaONThttps://github.com/chanzuckerberg/shastaShafin et al. 2020
VerkkoONT + PacBio + Illuminahttps://github.com/marbl/verkkoRautiainen et al. 2023
Assembly QC (N)AssemblyQCNAhttps://github.com/Plant-Food-Research-Open/assemblyqcRashid et al. 2024
BUSCONAhttps://gitlab.com/ezlab/buscoManni et al. 2021
FlaggerONT/PacBiohttps://github.com/mobinasri/flaggerLiao et al. 2023
MerquryIlluminahttps://github.com/marbl/merquryRhie et al. 2020
NucFreqONT/PacBiohttps://github.com/mrvollger/NucFreqVollger et al. 2019
QUAST-LGONT/PacBiohttps://quast.sourceforge.net/quast-lg.htmlMikheenko et al. 2018
Variant calling from assembly (O)DipcallNAhttps://github.com/lh3/dipcallLi et al. 2018
PAVNAhttps://github.com/EichlerLab/pavEbert et al. 2021
Graph genome tools (P)GiraffeNAhttps://github.com/vgteam/vgSirén et al. 2021
Graph Genome pipelineNAhttps://github.com/graph-genome/pipelineGuarracino et al. 2022
Minigraph-CactusNAhttps://github.com/ComparativeGenomicsToolkit/cactusHickey et al. 2024
PanGenieNAhttps://github.com/eblerjana/pangenieEbler et al. 2022
PGGBNAhttps://github.com/pangenome/pggbGarrison et al. 2024
PGR-TKNAhttps://github.com/GeneDx/pgr-tkChin et al. 2023
VGNAhttps://github.com/vgteam/vgGarrison et al. 2018

[i] Letters in parentheses correspond to Figure 2 workflow steps.