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Related Experiment Video

Updated: Jun 5, 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

Published on: August 20, 2021

High-quality draft assemblies of mammalian genomes from massively parallel sequence data.

Sante Gnerre¹, Iain Maccallum, Dariusz Przybylski

¹Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.

Proceedings of the National Academy of Sciences of the United States of America

|December 29, 2010

Summary

New ALLPATHS-LG software enables high-quality de novo genome assembly from massively parallel DNA sequencing data. This advance improves genome sequencing accuracy and scaffold size, making large genome sequencing more feasible.

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Last Updated: Jun 5, 2026

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Area of Science:

Genomics
Bioinformatics
Computational Biology

Background:

Massively parallel DNA sequencing generates billions of short reads cost-effectively.
Generating high-quality de novo genome assemblies for large, repeat-rich genomes remains challenging.
Existing assemblies from short reads are inferior to those from older, expensive capillary sequencing.

Purpose of the Study:

To develop an advanced algorithm for de novo genome assembly.
To apply the algorithm to massively parallel sequencing data from human and mouse genomes.
To evaluate the quality of the resulting genome assemblies.

Main Methods:

Development of the ALLPATHS-LG genome assembly algorithm.
Application of ALLPATHS-LG to Illumina sequencing data from human and mouse.
Analysis of assembly accuracy, contiguity, connectivity, and coverage.

Main Results:

ALLPATHS-LG produced draft genome assemblies with high base accuracy (≥99.95%).
Scaffold sizes approached those from capillary sequencing (N50: 11.5 Mb for human, 7.2 Mb for mouse).
Assemblies demonstrated good short-range contiguity, long-range connectivity, and genome coverage.

Conclusions:

ALLPATHS-LG significantly improves de novo genome assembly from short-read sequencing data.
The combination of sequencing technology and computational methods enhances large genome sequencing.
This breakthrough facilitates increased de novo sequencing of complex genomes.