Table 4.
Common computational tools for long-read sequencing data analysis.
| Bioinformatic Analysis |
Tool | Sequencing Strategy | References |
|---|---|---|---|
| Base calling | Guppy, Bonito | ONT | https://github.com/nanoporetech/ (accessed on 2 August 2022) |
| Generate CCS | PacBio | [242] | |
| Quality control | pycoQC, NanoPack | ONT | [239,240] |
| Isoseq3 | PacBio | https://github.com/PacificBiosciences/IsoSeq (accessed on 2 August 2022) | |
| Read-error correction | Canu | ONT | [243] |
| LoRMA | PacBio | [244] | |
| DNA methylation | pycoMeth, DeepSignal, Megalodon | ONT | [245,246]; https://github.com/nanoporetech/megalodon (accessed on 2 August 2022) |
| pb-CpG-tools | PacBio | https://github.com/PacificBiosciences/pb-CpG-tools (accessed on 2 August 2022) | |
| Alignment | minimap2, NGMLR | ONT | [117,247] |
| pbmm2 | PacBio | https://github.com/PacificBiosciences/pbmm2 (accessed on 2 August 2022) | |
| SNV calling | Longshot, DeepVariant | ONT, PacBio | [248,249] |
| SV calling | Sniffles, SVIM, SVIM-asm, cuteSV | ONT | [247,250,251,252] |
| pbsv | PacBio | https://github.com/PacificBiosciences/pbsv (accessed on 2 August 2022) | |
| De novo assembly | Flye, Shasta | ONT | [253,254] |
| Hifiasm, FALCON | PacBio | [255,256] | |
| Hybrid assembly | MaSuRCA, WENGAN | ONT, PacBio | [257,258] |
| Polishing | Racon, Medaka, Pilon | ONT | [259,260] |
| Pilon, Quiver, Arrow | PacBio | [260,261] |
SNV, small nucleotide variant; SV, structural variant; ONT, Oxford Nanopore Technologies; PacBio, Pacific Biosciences.