Summary of software tools for analyzing long reads in cancer
| Category | Tool name | Description | Reference |
|---|---|---|---|
| Alignment | NGMLR | Convex gap-cost scoring model to achieve long-read alignment | Sedlazeck et al. 2018 |
| minimap2 | Pairwise alignment method for long reads and large genomes | Li 2018 | |
| Winnowmap | Improvements in aligning long reads in repetitive regions | Jain et al. 2020 | |
| Small variant detection | ClairS | Deep learning method designed for detecting somatic small variants, primarily for ONT long-read data | Zheng et al. 2023 |
| DeepSomatic | Discovery of somatic small variants across multiple sequencing platforms | Park et al. 2024 | |
| SV calling | nanomonsv | Identification of somatic SVs at single-nucleotide resolution | Shiraishi et al. 2023 |
| SAVANA | Somatic SV and copy number aberrations caller for long reads | Elrick et al. 2024 | |
| SVision-pro | Neural network framework enabling somatic structural variant discovery and genotyping | Wang et al. 2024 | |
| Sniffles2 | Updated version of Sniffles; capable of identifying mosaic and population-level SVs using long reads | Smolka et al. 2024 | |
| Severus | Improved detection and characterization of somatic SVs in tumor genomes | Keskus et al. 2024 | |
| Variant phasing | WhatsHap | Phasing of SNVs and smaller indels | Martin et al. 2023 |
| LongPhase | Fast chromosome-scale phasing for both small and large variations | Lin et al. 2022 | |
| Methylation identification | DeepSignal | Detection of DNA methylation states from ONT long reads | Ni et al. 2019 |
| Uncalled4 | Toolkit for ONT signal alignment, analysis, and visualization, improving DNA and RNA modification detection | Kovaka et al. 2024 | |
| ccsmeth | DNA 5mCpGs caller for PacBio CCS data | Ni et al. 2023 | |
| Methylation phasing | NanoMethPhase | Phasing of 5mCpGs from ONT sequencing data | Akbari et al. 2021 |
| MethPhaser | Utilization of ONT methylation signals to extend SNV-based phasing | Fu et al. 2024 | |
| ccsmethphase | Nextflow pipeline for haplotype-aware methylation detection using PacBio CCS reads | Ni et al. 2023 |