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Related Concept Videos

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Updated: Feb 27, 2026

Sequencing of mRNA from Whole Blood using Nanopore Sequencing
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Rawsamble: overlapping raw nanopore signals using a hash-based seeding mechanism.

Can Firtina1,2, Maximilian Mordig3,4, Harun Mustafa3,5,6

  • 1Department of Information Technology and Electrical Engineering, ETH Zurich, Zurich, 8092, Switzerland.

Bioinformatics (Oxford, England)
|February 26, 2026
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Summary
This summary is machine-generated.

Rawsamble enables de novo genome assembly directly from raw nanopore signals, bypassing basecalling. This hash-based method significantly speeds up analysis and reduces memory usage for genomics research.

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Area of Science:

  • Genomics
  • Bioinformatics
  • Computational Biology

Background:

  • Raw nanopore signal analysis offers fast, resource-efficient genomics without basecalling.
  • Existing methods struggle with noisy raw signal comparisons for unknown genomes.
  • Direct analysis of raw signals without a reference genome is a key challenge.

Purpose of the Study:

  • To enable direct analysis of raw nanopore signals without a reference genome.
  • To develop a mechanism for identifying similarity between all raw signal pairs (all-vs-all overlapping).

Main Methods:

  • Proposed Rawsamble, a novel hash-based search mechanism for all-vs-all raw signal overlapping.
  • Utilized Rawsamble overlaps with the miniasm assembler for de novo assembly graph construction.
  • Evaluated performance across multiple genomes of varying sizes.

Main Results:

  • Achieved significant speedup (5.01× on average, up to 23.10×) and reduced peak memory usage (5.74× on average, up to 22.00×) compared to conventional pipelines.
  • Constructed de novo assemblies directly from raw signals, a first in the field.
  • Generated accurate unitigs up to 2.3 million bases long, comparable to state-of-the-art methods.

Conclusions:

  • Rawsamble facilitates efficient de novo genome assembly directly from raw nanopore signals.
  • The method offers substantial computational advantages over traditional basecalling-dependent pipelines.
  • Rawsamble represents a significant advancement for reference-free genomics analysis.