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Updated: Jun 6, 2026

Hybrid De Novo Genome Assembly for the Generation of Complete Genomes of Urinary Bacteria using Short- and Long-read Sequencing Technologies

Hybrid De Novo Genome Assembly for the Generation of Complete Genomes of Urinary Bacteria using Short- and Long-read Sequencing Technologies

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Scoring-and-unfolding trimmed tree assembler: concepts, constructs and comparisons.

Giuseppe Narzisi¹, Bud Mishra

¹Courant Institute of Mathematical Sciences, New York University, New York, NY 10012, USA. narzisi@nyu.edu

Bioinformatics (Oxford, England)

|November 20, 2010

Summary

This summary is machine-generated.

This study introduces the Scoring-and-Unfolding Trimmed Tree Assembler (SUTTA) for whole-genome sequence assembly (WGSA). SUTTA employs a constrained search to find exact solutions, improving accuracy over heuristic methods.

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Introductory Analysis and Validation of CUT&RUN Sequencing Data

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Introductory Analysis and Validation of CUT&RUN Sequencing Data

Introductory Analysis and Validation of CUT&RUN Sequencing Data

Published on: December 13, 2024

Area of Science:

Genomics
Bioinformatics
Computational Biology

Background:

Whole-genome sequence assembly (WGSA) has been historically limited to approximate greedy and heuristic methods due to its NP-complete nature (Shortest Common Superstring Problem).
Existing heuristic approaches for WGSA are often error-prone, especially for complex genomes, and their performance is highly dependent on input data quality and available long-range information.
These limitations have hindered the development of error-free WGSA pipelines.

Purpose of the Study:

To develop a novel framework for whole-genome sequence assembly that moves beyond approximate solutions.
To enable an exhaustive search of all possible genome layouts through a constrained search approach.
To introduce a method that combines various structural properties using score functions for accurate assembly.

Main Methods:

Developed the Scoring-and-Unfolding Trimmed Tree Assembler (SUTTA), a novel assembly framework.
Implemented a constrained search (Branch-and-Bound) to manage the computational complexity of exhaustive search.
Utilized score functions (oracles) that integrate diverse structural properties like transitivity and coverage to prune implausible sequence overlays.

Main Results:

Presented experimental results of SUTTA on bacterial genomes using next-generation sequencing data.
Demonstrated that SUTTA can potentially lead to an exhaustive search of all possible layouts, overcoming limitations of heuristic methods.
Showed that assembly quality is significantly influenced by the choice of the minimum overlap parameter (k).

Conclusions:

SUTTA offers a new framework for whole-genome sequence assembly, aiming for exact solutions rather than approximations.
The Branch-and-Bound strategy combined with scoring functions effectively tames the computational complexity of exhaustive genome assembly.
The study highlights the critical role of the minimum overlap parameter (k) in achieving high-quality genome assemblies.