Long-read sequencing

Software

cuteFC

GitHub: https://github.com/Meltpinkg/cuteFC

cuteSV

GitHub: https://github.com/tjiangHIT/cuteSV

pbmm2

GitHub: https://github.com/PacificBiosciences/pbmm2

pbsv

GitHub: https://github.com/PacificBiosciences/pbsv

RTG tools

GitHub: https://github.com/RealTimeGenomics/rtg-tools

Sniffles

GitHub, https://github.com/fritzsedlazeck/Sniffles

Truvari

GitHub: https://github.com/ACEnglish/truvari

Data sources

GIAB

Web: https://ftp.ncbi.nlm.nih.gov/giab/ftp/

The ONT PromethION dataset of the HG002 sample is here, https://ftp.ncbi.nlm.nih.gov/giab/ftp/data/AshkenazimTrio/HG002_NA24385_son/UCSC_Ultralong_OxfordNanopore_Promethion/

IGSR

Web: https://www.internationalgenome.org/

References

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.

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. 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