ModDotPlot-rapid and Interactive Visualization of Tandem Repeats

Overview

Journal Bioinformatics

Publisher Oxford University Press

Specialty Biology

Date 2024 Aug 7

PMID 39110522

Authors

Alexander P Sweeten

Michael C Schatz

Adam M Phillippy

Affiliations

Soon will be listed here.

Abstract

Motivation: A common method for analyzing genomic repeats is to produce a sequence similarity matrix visualized via a dot plot. Innovative approaches such as StainedGlass have improved upon this classic visualization by rendering dot plots as a heatmap of sequence identity, enabling researchers to better visualize multi-megabase tandem repeat arrays within centromeres and other heterochromatic regions of the genome. However, computing the similarity estimates for heatmaps requires high computational overhead and can suffer from decreasing accuracy.

Results: In this work, we introduce ModDotPlot, an interactive and alignment-free dot plot viewer. By approximating average nucleotide identity via a k-mer-based containment index, ModDotPlot produces accurate plots orders of magnitude faster than StainedGlass. We accomplish this through the use of a hierarchical modimizer scheme that can visualize the full 128 Mb genome of Arabidopsis thaliana in under 5 min on a laptop. ModDotPlot is bundled with a graphical user interface supporting real-time interactive navigation of entire chromosomes.

Availability And Implementation: ModDotPlot is available at https://github.com/marbl/ModDotPlot.

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References

Rhie A, Nurk S, Cechova M, Hoyt S, Taylor D, Altemose N . The complete sequence of a human Y chromosome. Nature. 2023; 621(7978):344-354. PMC: 10752217. DOI: 10.1038/s41586-023-06457-y. View

Kille B, Garrison E, Treangen T, Phillippy A . Minmers are a generalization of minimizers that enable unbiased local Jaccard estimation. Bioinformatics. 2023; 39(9). PMC: 10505501. DOI: 10.1093/bioinformatics/btad512. View

Vollger M, Kerpedjiev P, Phillippy A, Eichler E . StainedGlass: interactive visualization of massive tandem repeat structures with identity heatmaps. Bioinformatics. 2022; 38(7):2049-2051. PMC: 8963321. DOI: 10.1093/bioinformatics/btac018. View

Wlodzimierz P, Rabanal F, Burns R, Naish M, Primetis E, Scott A . Cycles of satellite and transposon evolution in Arabidopsis centromeres. Nature. 2023; 618(7965):557-565. DOI: 10.1038/s41586-023-06062-z. View

Sahlin K, Baudeau T, Cazaux B, Marchet C . A survey of mapping algorithms in the long-reads era. Genome Biol. 2023; 24(1):133. PMC: 10236595. DOI: 10.1186/s13059-023-02972-3. View

Makova K, Pickett B, Harris R, Hartley G, Cechova M, Pal K . The complete sequence and comparative analysis of ape sex chromosomes. Nature. 2024; 630(8016):401-411. PMC: 11168930. DOI: 10.1038/s41586-024-07473-2. View

Marcais G, Delcher A, Phillippy A, Coston R, Salzberg S, Zimin A . MUMmer4: A fast and versatile genome alignment system. PLoS Comput Biol. 2018; 14(1):e1005944. PMC: 5802927. DOI: 10.1371/journal.pcbi.1005944. View

Sedlazeck F, Lee H, Darby C, Schatz M . Piercing the dark matter: bioinformatics of long-range sequencing and mapping. Nat Rev Genet. 2018; 19(6):329-346. DOI: 10.1038/s41576-018-0003-4. View

Abdennur N, Mirny L . Cooler: scalable storage for Hi-C data and other genomically labeled arrays. Bioinformatics. 2019; 36(1):311-316. PMC: 8205516. DOI: 10.1093/bioinformatics/btz540. View

10.

Logsdon G, Rozanski A, Ryabov F, Potapova T, Shepelev V, Catacchio C . The variation and evolution of complete human centromeres. Nature. 2024; 629(8010):136-145. PMC: 11062924. DOI: 10.1038/s41586-024-07278-3. View

11.

Rautiainen M, Nurk S, Walenz B, Logsdon G, Porubsky D, Rhie A . Telomere-to-telomere assembly of diploid chromosomes with Verkko. Nat Biotechnol. 2023; 41(10):1474-1482. PMC: 10427740. DOI: 10.1038/s41587-023-01662-6. View

12.

Nurk S, Koren S, Rhie A, Rautiainen M, Bzikadze A, Mikheenko A . The complete sequence of a human genome. Science. 2022; 376(6588):44-53. PMC: 9186530. DOI: 10.1126/science.abj6987. View

13.

Naish M, Alonge M, Wlodzimierz P, Tock A, Abramson B, Schmucker A . The genetic and epigenetic landscape of the centromeres. Science. 2021; 374(6569):eabi7489. PMC: 10164409. DOI: 10.1126/science.abi7489. View

14.

Hera M, Pierce-Ward N, Koslicki D . Deriving confidence intervals for mutation rates across a wide range of evolutionary distances using FracMinHash. Genome Res. 2023; 33(7):1061-1068. PMC: 10538494. DOI: 10.1101/gr.277651.123. View

15.

Miga K, Newton Y, Jain M, Altemose N, Willard H, Kent W . Centromere reference models for human chromosomes X and Y satellite arrays. Genome Res. 2014; 24(4):697-707. PMC: 3975068. DOI: 10.1101/gr.159624.113. View

16.

Harris C, Millman K, van der Walt S, Gommers R, Virtanen P, Cournapeau D . Array programming with NumPy. Nature. 2020; 585(7825):357-362. PMC: 7759461. DOI: 10.1038/s41586-020-2649-2. View

17.

Maizel Jr J, Lenk R . Enhanced graphic matrix analysis of nucleic acid and protein sequences. Proc Natl Acad Sci U S A. 1981; 78(12):7665-9. PMC: 349330. DOI: 10.1073/pnas.78.12.7665. View

18.

Logsdon G, Eichler E . The Dynamic Structure and Rapid Evolution of Human Centromeric Satellite DNA. Genes (Basel). 2023; 14(1). PMC: 9859433. DOI: 10.3390/genes14010092. View

19.

Altemose N, Logsdon G, Bzikadze A, Sidhwani P, Langley S, Caldas G . Complete genomic and epigenetic maps of human centromeres. Science. 2022; 376(6588):eabl4178. PMC: 9233505. DOI: 10.1126/science.abl4178. View

20.

Das A, Schatz M . Sketching and sampling approaches for fast and accurate long read classification. BMC Bioinformatics. 2022; 23(1):452. PMC: 9624007. DOI: 10.1186/s12859-022-05014-0. View