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Research: Strong bias in long-read sequencing prevents assembly of Drosophila melanogaster Y-linked genes
- A. Bernardo Carvalho,
- Bernard Y. Kim,
- and Fabiana Uno
Genome Res. January 2026 36: 71-82; Published in Advance October 1, 2025, doi:10.1101/gr.280604.125
...region). This procedure reduced assembly complexity by including only reads from the region of interest. We initially attempted to assemble each region separately, using Canu (Koren et al. 2017) and Flye (Kolmogorov et al. 2019), with very poor results (small contigs or no contig at all; it must be added...
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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
...de novo assembly, offering significant advantages over traditional short-read approaches (Espinosa et al. 2024). Several long-read assembly tools have emerged, such as Canu (Koren et al. 2017), Flye (Kolmogorov et al. 2019), Hifiasm (Cheng et al. 2021), and Shasta (Shafin et al. 2020). Hifiasm (Cheng...
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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
....MethodsThe original Verkko pipeline consisted of six main steps, with module dependencies given in parentheses: homopolymer compression and correction of LA reads (HiCanu) (Nurk et al. 2020), LA multiplex De Bruijn graph construction (MBG) (Rautiainen and Marschall 2021), alignment of UL reads to the LA graph (Graph...
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Research: Long-read genome assembly of the insect model organism Tribolium castaneum reveals spread of satellite DNA in gene-rich regions by recurrent burst events
- Marin Volarić,
- Evelin Despot-Slade,
- Damira Veseljak,
- Brankica Mravinac,
- and Nevenka Meštrović
Genome Res. November 2024 34: 1878-1894; Published in Advance October 22, 2024, doi:10.1101/gr.279225.124
...). This larger size likely reflects many sequences that could not be linked to correct chromosomal positions and, as a result, cannot be accurately evaluated. To verify the size and repetitiveness in silico, the k-mer frequencies of the corrected reads generated during the Canu assembly process using the find...
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Research: Whole-genome long-read sequencing downsampling and its effect on variant-calling precision and recall
- William T. Harvey,
- Peter Ebert,
- Jana Ebler,
- Peter A. Audano,
- Katherine M. Munson,
- Kendra Hoekzema,
- David Porubsky,
- Christine R. Beck,
- Tobias Marschall,
- Kiran Garimella,
- and Evan E. Eichler
Genome Res. December 2023 33: 2029-2040; Published in Advance December 7, 2023, doi:10.1101/gr.278070.123
...and phasing. Methods such as Shasta (Shafin et al. 2020), wtdbg2 (Ruan and Li 2020), and Canu (Koren et al. 2017) show considerable promise, yet currently contiguous, haplotype-phased assemblies are not as easily generated and thus have not been used as frequently in recent studies.SNV calling with assembly...
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Research: Highly complete long-read genomes reveal pangenomic variation underlying yeast phenotypic diversity
- Cory A. Weller,
- Ilya Andreev,
- Michael J. Chambers,
- Morgan Park,
- NISC Comparative Sequencing Program,
- Joshua S. Bloom,
- and Meru J. Sadhu
Genome Res. May 2023 33: 729-740; Published in Advance May 1, 2023, doi:10.1101/gr.277515.122
...purification kit (Lucigen) and sequenced on a Sequel II sequencer (PacBio) to produce circular consensus sequence (CCS) reads, as detailed in the Supplemental Methods.CCS reads from each sample were assembled using Canu v. 2.2 (parameters Size = 12mb -pacbio-hifi) (Koren et al. 2017). When read coverage...
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Method: Improved assembly of noisy long reads by k-mer validation
- Antonio Bernardo Carvalho,
- Eduardo G. Dupim,
- and Gabriel Goldstein
Genome Res. December 2016 26: 1710-1720; Published in Advance October 7, 2016, doi:10.1101/gr.209247.116
...in the range of 60%–90% (Berlin et al. 2015).MHAPis thedefaultalignerused inthePBcRpipeline,which, after correcting the reads, feeds them into the Celera Assembler. Currently PBcR (and its recent substitute, Canu) (Koren et al. 2016) is the pipeline that requires the smaller computational infrastructure...
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Resource: Long-read sequencing reveals intra-species tolerance of substantial structural variations and new subtelomere formation in C. elegans
- Chuna Kim,
- Jun Kim,
- Sunghyun Kim,
- Daniel E. Cook,
- Kathryn S. Evans,
- Erik C. Andersen,
- and Junho Lee
Genome Res. June 2019 29: 1023-1035; Published in Advance May 23, 2019, doi:10.1101/gr.246082.118
...://github.com/PacificBiosciences/GenomicConsensus). We repeated this process with the Quiver-polished assembly instead of the Canu-only one. Next, to remove bacterial sequence contamination, we aligned the contigs with 3000 bacterial s downloaded at European Nucleotide Archive (ENA) (on March 30, 2018) from ftp...
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Method: MinION-based long-read sequencing and assembly extends the Caenorhabditis elegans reference genome
- John R. Tyson,
- Nigel J. O'Neil,
- Miten Jain,
- Hugh E. Olsen,
- Philip Hieter,
- and Terrance P. Snutch
Genome Res. February 2018 28: 266-274; Published in Advance December 22, 2017, doi:10.1101/gr.221184.117
.... 2017. Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation. Genome Res 27: 722–736. ↵Kurtz S, Phillippy A, Delcher AL, Smoot M, Shumway M, Antonescu C, Salzberg SL. 2004. Versatile and open software for comparing large s. Genome Biol 5: R12. ↵Leibowitz ML...
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Method: Efficient mapping of accurate long reads in minimizer space with mapquik
- Bariş Ekim,
- Kristoffer Sahlin,
- Paul Medvedev,
- Bonnie Berger,
- and Rayan Chikhi
Genome Res. July 2023 33: 1188-1197; Published in Advance June 30, 2023, doi:10.1101/gr.277679.123
.... 2022). A significant part of the minimap2 and Winnowmap2 running times are in their seeding and chaining steps (Kalikar et al. 2022). These state-of-the-art long-read alignment tools are sensitive and accurate, but their underlying seed constructs (k-mers) are tailored to noisy reads. These small seed...
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