Table 1.
List of methods for long-read analysis and its function
| Function | Tool | Technology | GitHub | Citation |
|---|---|---|---|---|
| Basecalling (A) | CCS | PacBio | https://github.com/PacificBiosciences/ccs | |
| Dorado | ONT | https://github.com/nanoporetech/dorado | ||
| Google Deep Consensus | PacBio | https://github.com/google/deepconsensus | Baid et al. 2023 | |
| Reads QC (B) | LongReadSum | ONT/PacBio | https://github.com/WGLab/LongReadSum | |
| LongQC | ONT/PacBio | https://github.com/yfukasawa/LongQC | Fukasawa et al. 2020 | |
| NanoPack | ONT/PacBio | https://github.com/wdecoster/nanopack | De Coster et al. 2018 | |
| Alignment (C) | LRA | ONT/PacBio | https://github.com/ChaissonLab/LRA | Ren and Chaisson 2021 |
| minimap2 | ONT/PacBio | https://github.com/lh3/minimap2 | Li 2018, 2021 | |
| NGMLR | ONT/PacBio | https://github.com/philres/ngmlr | Sedlazeck et al. 2018b | |
| pbmm2 | PacBio | https://github.com/PacificBiosciences/pbmm2 | ||
| VACmap | ONT/PacBio | https://github.com/micahvista/VACmap | Ding et al. 2024 | |
| Vulcan | ONT/PacBio | https://gitlab.com/treangenlab/vulcan | Fu et al. 2021 | |
| Winnowmap2 | ONT/PacBio | https://github.com/marbl/Winnowmap | Jain et al. 2022 | |
| Alignment QC (D) | NanoPack | ONT/PacBio | https://github.com/wdecoster/nanopack | De Coster et al. 2018 |
| Sambamba | ONT/PacBio | https://github.com/biod/sambamba | Tarasov et al. 2015 | |
| SAMtools | ONT/PacBio | https://github.com/samtools/samtools | Li et al. 2009 | |
| SNV & indels calling (E) | Clair3 | ONT/PacBio | https://github.com/HKU-BAL/Clair3 | Zheng et al. 2022 |
| DeepSomatic | Illumina/ONT/PacBio | https://github.com/google/deepsomatic | Park et al. 2024 | |
| DeepVariant | ONT/PacBio | https://github.com/google/deepvariant | Poplin et al. 2018 | |
| Longshot | ONT/PacBio | https://github.com/pjedge/longshot | Edge and Bansal 2019 | |
| SV calling (F) | cuteSV | ONT/PacBio | https://github.com/tjiangHIT/cuteSV | Jiang et al. 2020 |
| DELLY | ONT/PacBio/Illumina | https://github.com/dellytools/delly?tab=readme-ov-file | Rausch et al. 2012 | |
| NanomonSV | ONT/PacBio | https://github.com/friend1ws/nanomonsv | Shiraishi et al. 2023 | |
| pbsv | PacBio | https://github.com/PacificBiosciences/pbsv | ||
| Sawfish | PacBio | https://github.com/PacificBiosciences/sawfish | Saunders et al. 2024 | |
| Severus | ONT/PacBio | https://github.com/KolmogorovLab/Severus | Keskus et al. 2024 | |
| Sniffles2 | ONT/PacBio | https://github.com/fritzsedlazeck/Sniffles | Smolka et al. 2024 | |
| SAVANA | ONT/PacBio | https://github.com/cortes-ciriano-lab/savana | Elrick et al. 2024 | |
| SVision | ONT/PacBio | https://github.com/xjtu-omics/SVision | Lin et al. 2022b | |
| Copy number variants (G) | HiFiCNV | PacBio | https://github.com/PacificBiosciences/HiFiCNV | |
| Spectre | ONT/PacBio | https://github.com/fritzsedlazeck/Spectre | ||
| Tandem repeat (TRs) (H) | Medaka | ONT | https://github.com/nanoporetech/medaka | Lee et al. 2021 |
| pathSTR | ONT | https://github.com/wdecoster/pathSTR | De Coster et al. 2024 | |
| Straglr | ONT | https://github.com/bcgsc/straglr | Chiu et al. 2021 | |
| StrSpy | ONT | https://github.com/unique379r/strspy | Hall et al. 2022 | |
| TRGT | PacBio | https://github.com/PacificBiosciences/trgt | Dolzhenko et al. 2024 | |
| Genotyping (I) | kanpig | ONT/PacBio | https://github.com/ACEnglish/kanpig | English et al. 2024a |
| SVJedi | ONT/PacBio | https://github.com/llecompte/SVJedi | Romain and Lemaitre 2023 | |
| Downstream analysis—phasing (J) | HapCUT2 | ONT/PacBio | https://github.com/vibansal/HapCUT2 | Edge et al. 2017 |
| HiPhase | PacBio | https://github.com/PacificBiosciences/HiPhase | Holt et al. 2024 | |
| WhatsHap | ONT/PacBio | https://github.com/whatshap/whatshap | Martin et al. 2023 | |
| Downstream analysis—variant annotation (K) | AnnotSV | NA | https://github.com/lgmgeo/AnnotSV | Geoffroy et al. 2018 |
| ANNOVAR | NA | http://annovar.openbioinformatics.org/ | Wang et al. 2010 | |
| CADD | NA | https://cadd.gs.washington.edu/ | Kircher et al. 2014 | |
| CADD-SV | NA | https://github.com/kircherlab/CADD-SV | Kleinert and Kircher 2022 | |
| DANN | NA | https://cbcl.ics.uci.edu/public_data/DANN/ | Quang et al. 2015 | |
| PolyPhen-2 | NA | http://genetics.bwh.harvard.edu/pph2/ | Adzhubei et al. 2013 | |
| SIFT | NA | https://sift.bii.a-star.edu.sg/ | Sim et al. 2012 | |
| SnpEff | NA | https://pcingola.github.io/SnpEff/ | Cingolani et al. 2012 | |
| SvAnna | ONT/PacBio | https://github.com/monarch-initiative/SvAnna | Danis et al. 2022 | |
| SVAFotate | NA | https://github.com/fakedrtom/SVAFotate | Nicholas et al. 2022 | |
| VEP | NA | https://github.com/Ensembl/ensembl-vep | Hunt et al. 2022 | |
| Downstream analysis—methylation calling (L) | Dorado | ONT | https://github.com/nanoporetech/dorado | |
| fibertools-rs/ft | PacBio | https://github.com/fiberseq/fibertools-rs | Jha et al. 2024 | |
| Jasmine | PacBio | https://github.com/PacificBiosciences/jasmine | ||
| Modkit | ONT | https://github.com/nanoporetech/modkit | ||
| Assembly (M) | Canu | ONT/PacBio | https://github.com/marbl/canu | Koren et al. 2017 |
| Flye | ONT | https://github.com/mikolmogorov/Flye | Konings et al. 2024 | |
| hifiasm | ONT/PacBio | https://github.com/chhylp123/hifiasm | Cheng et al. 2021 | |
| Shasta | ONT | https://github.com/chanzuckerberg/shasta | Shafin et al. 2020 | |
| Verkko | ONT + PacBio + Illumina | https://github.com/marbl/verkko | Rautiainen et al. 2023 | |
| Assembly QC (N) | AssemblyQC | NA | https://github.com/Plant-Food-Research-Open/assemblyqc | Rashid et al. 2024 |
| BUSCO | NA | https://gitlab.com/ezlab/busco | Manni et al. 2021 | |
| Flagger | ONT/PacBio | https://github.com/mobinasri/flagger | Liao et al. 2023 | |
| Merqury | Illumina | https://github.com/marbl/merqury | Rhie et al. 2020 | |
| NucFreq | ONT/PacBio | https://github.com/mrvollger/NucFreq | Vollger et al. 2019 | |
| QUAST-LG | ONT/PacBio | https://quast.sourceforge.net/quast-lg.html | Mikheenko et al. 2018 | |
| Variant calling from assembly (O) | Dipcall | NA | https://github.com/lh3/dipcall | Li et al. 2018 |
| PAV | NA | https://github.com/EichlerLab/pav | Ebert et al. 2021 | |
| Graph genome tools (P) | Giraffe | NA | https://github.com/vgteam/vg | Sirén et al. 2021 |
| Graph Genome pipeline | NA | https://github.com/graph-genome/pipeline | Guarracino et al. 2022 | |
| Minigraph-Cactus | NA | https://github.com/ComparativeGenomicsToolkit/cactus | Hickey et al. 2024 | |
| PanGenie | NA | https://github.com/eblerjana/pangenie | Ebler et al. 2022 | |
| PGGB | NA | https://github.com/pangenome/pggb | Garrison et al. 2024 | |
| PGR-TK | NA | https://github.com/GeneDx/pgr-tk | Chin et al. 2023 | |
| VG | NA | https://github.com/vgteam/vg | Garrison et al. 2018 |
-
Letters in parentheses correspond to Figure 2 workflow steps.
