Stefano Lonardi | How to “Squeeze” the Best Genome Assembly From Your HiFi Reads | CGSI 2023

Related papers:

[1] Nurk, S., Walenz, B.P, et al. (2020) HiCanu: accurate assembly of segmental duplications, satellites, and allelic variants from high-fidelity long reads. Genome Research 30, 9

[2] Cheng, H., Concepcion, G.T., Feng, X., Zhang, H., Li H. (2021) Haplotype-resolved de novo assembly using phased assembly graphs with Hifiasm. Nature Methods, 18:170-175

[3] Chakravarty, S., Logsdon, G., Lonardi, S., (2023) RAmbler: de novo genome assembly of complex repetitive regions, bioRxiv 2023.05.26.542525

[4] Logsdon, G., Vollger, M., et al. (2021) The structure, function and evolution of a complete human chromosome 8. Nature 593

[5] Pan, W., Jiang, T., Lonardi, S., (2020) OMGS: Optical Map-based Genome Scaffolding.

Proceedings of RECOMB 2019 and Journal of Computational Biology, 27(4): 519-533

[6] Pan, W., Wanamaker, S., et al, (2018) Novo&Stitch: Accurate Reconciliation of Genome Assemblies via Optical Maps. Proceedings of ISMB 2018 - Conference on Intelligent Systems for Molecular Biology, July 6-10, Chicago, 2018. Special Issue of Bioinformatics, 34(13): i43–i51, 2018 doi:10.1093/bioinformatics/bty255