Polarization gratings aided common-path Hilbert holotomography for high-throughput lipid droplets content assay DOI Creative Commons
Piotr Zdańkowski, Julianna Winnik, Mikołaj Rogalski

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: June 17, 2024

Abstract In this contribution we present a novel polarization gratings aided common-path Hilbert holotomography (CP-HHT) for high-throughput 3D refractive index imaging. Addressing limitations in current methods, leverage the extended space-bandwidth product (SBP) through robust phase demodulation using spiral transform. Thanks to application of diffraction our system enables fully tailored holographic settings such as fringe density and shear, thus allowing flexible hologram demodulation, while maintaining simplicity robustness. The performance is tested on 3D-printed (using two-photon polymerization) brain phantom fixed HeLa cells supplemented with cholesterol oleic acids. Reconstruction analysis indicates that method provides comparable results resolution Fourier transform significantly expanded measurement throughput. Our CP-HHT approach demonstrates unique (not possible by fluorescence) (especially when compared cryogenic electron microscopy) capability differentiate between esters vs. triacylglycerol (TAG) rich lipid droplets (LDs), has potential label-free biological research at sub-cellular level. quantitative LDs’ emphasizes method’s sensitivity distinguishing LDs different neutral content, offering new insights into LD heterogeneity, reinforcing versatility applicability broader bioimaging applications.

Language: Английский

Genomics in the long-read sequencing era DOI Creative Commons

Erwin L. van Dijk,

Delphine Naquin, Kévin Gorrichon

et al.

Trends in Genetics, Journal Year: 2023, Volume and Issue: 39(9), P. 649 - 671

Published: May 23, 2023

Language: Английский

Citations

73
Genome assembly in the telomere-to-telomere era DOI
Heng Li, Richard Durbin

Nature Reviews Genetics, Journal Year: 2024, Volume and Issue: 25(9), P. 658 - 670

Published: April 22, 2024

Language: Английский

Citations

68
Linear time complexity de novo long read genome assembly with GoldRush DOI Creative Commons
Johnathan Wong, Lauren Coombe, Vladimir Nikolić

et al.

Nature Communications, Journal Year: 2023, Volume and Issue: 14(1)

Published: May 22, 2023

Current state-of-the-art de novo long read genome assemblers follow the Overlap-Layout-Consensus paradigm. While read-to-read overlap - its most costly step was improved in modern assemblers, these tools still often require excessive RAM when assembling a typical human dataset. Our work departs from this paradigm, foregoing all-vs-all sequence alignments favor of dynamic data structure implemented GoldRush, assembly algorithm with linear time complexity. We tested GoldRush on Oxford Nanopore Technologies sequencing datasets different base error profiles sourced three cell lines, rice, and tomato. Here, we show that achieves scaffold NGA50 lengths 18.3-22.2, 0.3 2.6 Mbp, for genomes human, tomato, respectively, assembles each within day, using at 54.5 GB random-access memory, demonstrating scalability our paradigm implementation.

Language: Английский

Citations

18
Gapless assembly of complete human and plant chromosomes using only nanopore sequencing DOI Open Access
Sergey Koren, Zhigui Bao, Andrea Guarracino

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: March 17, 2024

The combination of ultra-long Oxford Nanopore (ONT) sequencing reads with long, accurate PacBio HiFi has enabled the completion a human genome and spurred similar efforts to complete genomes many other species. However, this approach for complete, "telomere-to-telomere" assembly relies on multiple platforms, limiting its accessibility. ONT "Duplex" reads, where both strands DNA are read improve quality, promise high per-base accuracy. To evaluate new data type, we generated Duplex three widely-studied genomes: HG002, Solanum lycopersicum Heinz 1706 (tomato), Zea mays B73 (maize). For diploid, heterozygous HG002 genome, also used "Pore-C" chromatin contact mapping completely phase haplotypes. We found accuracy be sequencing, but lengths tens kilobases longer, Pore-C compatible existing diploid algorithms. This length enables construction high-quality initial assembly, which can then further resolved using finally phased into chromosome-scale haplotypes Pore-C. resulting assemblies have base exceeding 99.999% (Q50) near-perfect continuity, most chromosomes assembled as single contigs. conclude that is viable alternative de novo potential provide single-instrument solution reconstruction genomes.

Language: Английский

Citations

8
Whole-genome long-read sequencing downsampling and its effect on variant-calling precision and recall DOI Creative Commons
William T. Harvey, Peter Ebert, Jana Ebler

et al.

Genome Research, Journal Year: 2023, Volume and Issue: 33(12), P. 2029 - 2040

Published: Dec. 1, 2023

Advances in long-read sequencing (LRS) technologies continue to make whole-genome more complete, affordable, and accurate. LRS provides significant advantages over short-read approaches, including phased de novo genome assembly, access previously excluded genomic regions, discovery of complex structural variants (SVs) associated with disease. Limitations remain respect cost, scalability, platform-dependent read accuracy the tradeoffs between sequence coverage sensitivity variant are important experimental considerations for application LRS. We compare genetic variant-calling precision recall Oxford Nanopore Technologies (ONT) Pacific Biosciences (PacBio) HiFi platforms a range coverages. For read-based applications, begins plateau around 12-fold majority called reasonable (F

Language: Английский

Citations

14
Efficient near telomere-to-telomere assembly of Nanopore Simplex reads DOI Creative Commons
Haoyu Cheng, Han Qu, Sean K. McKenzie

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2025, Volume and Issue: unknown

Published: April 17, 2025

ABSTRACT Telomere-to-telomere (T2T) assembly is the ultimate goal for de novo genome assembly. Existing algorithms capable of near T2T all require Oxford Nanopore Technologies (ONT) ultra-long reads which are costly and experimentally challenging to obtain thus often unavailable samples without established cell lines. Here, we introduce hifiasm (ONT), first algorithm that can produce assemblies from standard ONT Simplex reads, eliminating need sequencing. Compared existing methods, reduces computational demands by an order magnitude reconstructs more chromosomes telomere on same datasets. This advancement substantially broadens feasibility applications previously limited high cost experimental requirement reads.

Language: Английский

Citations

0
Whole-genome long-read sequencing downsampling and its effect on variant calling precision and recall DOI Creative Commons
William T. Harvey, Peter Ebert, Jana Ebler

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2023, Volume and Issue: unknown

Published: May 4, 2023

Advances in long-read sequencing (LRS) technology continue to make whole-genome more complete, affordable, and accurate. LRS provides significant advantages over short-read approaches, including phased

Language: Английский

Citations

8
Graphasing: phasing diploid genome assembly graphs with single-cell strand sequencing DOI Creative Commons
Mir Henglin,

Maryam Ghareghani,

William T. Harvey

et al.

Genome biology, Journal Year: 2024, Volume and Issue: 25(1)

Published: Oct. 10, 2024

Abstract Haplotype information is crucial for biomedical and population genetics research. However, current strategies to produce de novo haplotype-resolved assemblies often require either difficult-to-acquire parental data or an intermediate haplotype-collapsed assembly. Here, we present Graphasing, a workflow which synthesizes the global phase signal of Strand-seq with assembly graph topology chromosome-scale haplotypes diploid genomes. Graphasing readily integrates any that both outputs has haplotype mode. performs comparably trio phasing in contiguity, accuracy, quality, outperforms Hi-C generates human over 18 chromosome-spanning haplotypes.

Language: Английский

Citations

2
Phasing Diploid Genome Assembly Graphs with Single-Cell Strand Sequencing DOI Creative Commons
Mir Henglin,

Maryam Ghareghani,

William T. Harvey

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Feb. 16, 2024

Haplotype information is crucial for biomedical and population genetics research. However, current strategies to produce

Language: Английский

Citations

1
Polarization gratings aided common-path Hilbert holotomography for high-throughput lipid droplets content assay DOI Creative Commons
Piotr Zdańkowski, Julianna Winnik, Mikołaj Rogalski

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: June 17, 2024

Abstract In this contribution we present a novel polarization gratings aided common-path Hilbert holotomography (CP-HHT) for high-throughput 3D refractive index imaging. Addressing limitations in current methods, leverage the extended space-bandwidth product (SBP) through robust phase demodulation using spiral transform. Thanks to application of diffraction our system enables fully tailored holographic settings such as fringe density and shear, thus allowing flexible hologram demodulation, while maintaining simplicity robustness. The performance is tested on 3D-printed (using two-photon polymerization) brain phantom fixed HeLa cells supplemented with cholesterol oleic acids. Reconstruction analysis indicates that method provides comparable results resolution Fourier transform significantly expanded measurement throughput. Our CP-HHT approach demonstrates unique (not possible by fluorescence) (especially when compared cryogenic electron microscopy) capability differentiate between esters vs. triacylglycerol (TAG) rich lipid droplets (LDs), has potential label-free biological research at sub-cellular level. quantitative LDs’ emphasizes method’s sensitivity distinguishing LDs different neutral content, offering new insights into LD heterogeneity, reinforcing versatility applicability broader bioimaging applications.

Language: Английский

Citations

0