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Method: Verkko2 integrates proximity-ligation data with long-read De Bruijn graphs for efficient telomere-to-telomere genome assembly, phasing, and scaffolding
- Dmitry Antipov,
- Mikko Rautiainen,
- Sergey Nurk,
- Brian P. Walenz,
- Steven J. Solar,
- Adam M. Phillippy,
- and Sergey Koren
Genome Res. July 2025 35: 1583-1594; Published in Advance May 19, 2025, doi:10.1101/gr.280383.124
...the most complex repeats, this project relied on the semimanual combination of long, accurate Pacific Biosciences (PacBio) HiFi and ultralong Oxford Nanopore Technologies sequencing reads. The Verkko assembler later automated this process, achieving complete assemblies for approximately half...
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Mini-Review: A Hitchhiker's Guide to long-read genomic analysis
- Medhat Mahmoud,
- Daniel P. Agustinho,
- and Fritz J. Sedlazeck
Genome Res. April 2025 35: 545-558; doi:10.1101/gr.279975.124
...for methylation.Initially, the adoption of long-read sequencing technologies suffered from both high error rates, at times up to 30%, and high costs, which have so far been significantly reduced over time (Fig. 1B). Currently, PacBio HiFi and ONT generate highly accurate long reads, exceeding 99% accuracy...

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