Long-read sequencing

Company sites

• AWS, https://github.com/aws
• ONT, https://nanoporetech.com/
• PacBio, https://www.pacb.com/

Software

• AWS CLI Command Reference, https://docs.aws.amazon.com/cli/latest/
• cuteFC, https://github.com/Meltpinkg/cuteFC
• cuteSV, https://github.com/tjiangHIT/cuteSV
• GAS power calculator, https://csg.sph.umich.edu/abecasis/gas_power_calculator/index.html
• Illumina, https://github.com/Illumina (hap.py)
• minimap2, https://github.com/lh3/minimap2
• ONT, https://github.com/nanoporetech
• pbmm2, https://github.com/PacificBiosciences/pbmm2
• pbsv, https://github.com/PacificBiosciences/pbsv
• RTG tools, https://github.com/RealTimeGenomics/rtg-tools
• Sniffles, https://github.com/fritzsedlazeck/Sniffles
• Stragli, https://github.com/philres/straglr
• Truvari, https://github.com/ACEnglish/truvari

Data sources

• ONT at AWS, https://registry.opendata.aws/ont-open-data/
• EPI2ME at ONT, https://epi2me.nanoporetech.com/dataindex/
• EPI2ME at GitHub, https://github.com/epi2me-labs
• GIAB, https://ftp.ncbi.nlm.nih.gov/giab/ftp/
  • ONT PromethION HG002 sample, https://ftp.ncbi.nlm.nih.gov/giab/ftp/data/AshkenazimTrio/HG002_NA24385_son/UCSC_Ultralong_OxfordNanopore_Promethion/
  • Reference sample, https://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/data/AshkenazimTrio/HG002_NA24385_son/PacBio_HiFi-Revio_20231031/
  • GRCh38_v3 Reference, https://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/release/references/GRCh38/
• IGSR, https://www.internationalgenome.org/

References

Genome Res special issues: 2024, 2025.

Bolognini D, et al. VISOR: a versatile haplotype-aware structural variant simulator for short- and long-read sequencing, Bioinformatics, 36(4), 1267–1269 (2020), https://doi.org/10.1093/bioinformatics/btz719

Jiang T, et al. Long-read-based human genomic structural variation detection with cuteSV. Genome Biol 21, 189 (2020). https://doi.org/10.1186/s13059-020-02107-y. The paper has scripts for various software.

Kirsche M, et al. Jasmine and Iris: population-scale structural variant comparison and analysis. Nat Methods 20, 408–417 (2023). https://doi.org/10.1038/s41592-022-01753-3

Smolka M, et al. Detection of mosaic and population-level structural variants with Sniffles2. Nat Biotechnol 42, 1571–1580 (2024). https://doi.org/10.1038/s41587-023-02024-y

Xia LC, et al. SVEngine: an efficient and versatile simulator of genome structural variations with features of cancer clonal evolution, GigaScience, 7(7), giy081 (2018), https://doi.org/10.1093/gigascience/giy081

Yuan N, Jia P. Comprehensive assessment of long-read sequencing platforms and calling algorithms for detection of copy number variation, Briefings in Bioinformatics, Volume 25, Issue 5, September 2024, bbae441, https://doi.org/10.1093/bib/bbae441. The paper includes an overview of software.

Zook JM, et al. A robust benchmark for detection of germline large deletions and insertions. Nat Biotechnol 38, 1347–1355 (2020). https://doi.org/10.1038/s41587-020-0538-8