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Spindle Assembly02:50

Spindle Assembly

Spindle assembly occurs through three, often coexisting, pathways – the centrosome-mediated pathway, the chromatin-mediated pathway, and the microtubule-mediated pathway – collectively contributing to form a robust spindle apparatus.
In most cells, centrosomes are the primary microtubule nucleation centers. In the centrosome-mediated pathway, the G2-prophase transition triggers centrosome maturation and increased microtubule nucleation. Progressive nucleation results in a microtubule array...

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Related Experiment Video

Updated: May 12, 2026

Convergent Polishing: A Simple, Rapid, Full Aperture Polishing Process of High Quality Optical Flats & Spheres
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Highly accurate assembly polishing with DeepPolisher.

Mira Mastoras1, Mobin Asri1, Lucas Brambrink2

  • 1UC Santa Cruz Genomics Institute, University of California, Santa Cruz, California 95060, USA.

Genome Research
|May 19, 2025
PubMed
Summary
This summary is machine-generated.

DeepPolisher, a new AI model, significantly improves genome assembly accuracy by reducing errors by half. It uses PacBio HiFi and Oxford Nanopore Technologies data for precise base-level corrections, enhancing biological research.

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Area of Science:

  • Genomics
  • Bioinformatics
  • Computational Biology

Background:

  • High-quality genome assemblies are crucial for biological research.
  • Existing assembly polishing methods face challenges in balancing over- and under-polishing.
  • Technological limitations in genome sequencing introduce errors into assemblies.

Purpose of the Study:

  • To introduce DeepPolisher, an encoder-only transformer model for accurate genome assembly polishing.
  • To develop a pipeline that leverages both PacBio HiFi and Oxford Nanopore Technologies (ONT) data for improved phasing and error correction.
  • To enhance the accuracy of diploid genome assemblies by addressing heterozygous variant miscalls.

Main Methods:

  • Developed DeepPolisher, a transformer model predicting sequence corrections using PacBio HiFi read alignments.
  • Introduced PHAsing Reads in Areas Of Homozygosity (PHARAOH) using ultralong ONT data for accurate phasing.
  • Applied the DeepPolisher pipeline to 180 Human Pangenome Reference Consortium (HPRC) assemblies.

Main Results:

  • The DeepPolisher pipeline reduced assembly errors by approximately 50%, primarily decreasing indel errors.
  • Achieved an average predicted quality value (QV) improvement of 3.4 (54% error reduction) across HPRC assemblies.
  • Successfully addressed challenges in phasing and correctly introduced heterozygous edits in previously homozygous regions.

Conclusions:

  • DeepPolisher offers a significant advancement in genome assembly polishing, substantially improving accuracy.
  • The integration of PacBio HiFi and ONT data within the PHARAOH method enhances the reliability of heterozygous variant detection.
  • This pipeline provides a robust solution for error correction in large-scale genomics projects, exemplified by its application to HPRC data.