Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • Research Briefing
  • Published:

Creating diploid assemblies from Nanopore and Illumina reads with hypo-assembler

Nature Methods volume 21, pages 560–561 (2024)Cite this article

Subjects

Diploid assembly is a difficult task that requires several types of genomic sequencing data, including — but not limited to — HiFi reads and parental sequences. Hypo-assembler, an assembly algorithm, uses high quality solid k-mers extracted from Illumina data alongside Nanopore reads to produce a high-quality diploid assembly using only Nanopore and Illumina data.

This is a preview of subscription content, access via your institution

Access options

Buy this article

  • Purchase on Springer Link
  • Instant access to full article PDF
Buy now

Prices may be subject to local taxes which are calculated during checkout

Fig. 1: Overview of the hypo-assembler algorithm.

References

  1. Cheng, H. et al. Haplotype-resolved assembly of diploid genomes without parental data. Nat. Biotechnol. 40, 1332–1335 (2022). This paper presents HiFiAsm, a HiFi-based haplotype-resolved assembler.

    Article  CAS  PubMed  Google Scholar 

  2. Koren, S. et al. De novo assembly of haplotype-resolved genomes with trio binning. Nat. Biotechnol. 36, 1174–1182 (2018). This paper presents TrioCanu, a trio-based haplotype-resolved assembler.

    Article  CAS  Google Scholar 

  3. Ariyaratne, P. N. et al. PE-Assembler: de novo assembler using short paired-end reads. Bioinformatics 27, 167–174 (2011). This paper is a previous use of the idea of solid k-mers.

    Article  CAS  PubMed  Google Scholar 

  4. Nurk, S. et al. The complete sequence of a human genome. Science 376, 44–53 (2022). The paper presents CHM13, a complete human reference genome.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  5. Jarvis, E. D. et al. Semi-automated assembly of high-quality diploid human reference genomes. Nature 611, 519–531 (2022). This paper presents the incomplete HG002 reference genome used in the evaluation.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

Download references

Additional information

Publisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

This is a summary of: Darian, J. C. et al. Constructing telomere-to-telomere diploid genome by polishing haploid nanopore-based assembly. Nat. Methods https://doi.org/10.1038/s41592-023-02141-1 (2024).

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Creating diploid assemblies from Nanopore and Illumina reads with hypo-assembler. Nat Methods 21, 560–561 (2024). https://doi.org/10.1038/s41592-023-02142-0

Download citation

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/s41592-023-02142-0

Search

Advanced search

Quick links

Nature Briefing AI and Robotics

Sign up for the Nature Briefing: AI and Robotics newsletter — what matters in AI and robotics research, free to your inbox weekly.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing: AI and Robotics