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REAPR: a universal tool for genome assembly evaluation.

Martin Hunt, Taisei Kikuchi, Mandy Sanders

|May 29, 2013

Summary

REAPR is a new tool that precisely identifies errors in genome assemblies without needing a reference sequence. This allows for accurate, quantitative comparison of genome assembly quality.

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Area of Science:

Genomics
Bioinformatics
Computational Biology

Background:

Reliable assessment of genome sequence data accuracy is currently lacking.
Existing methods for genome assembly evaluation are qualitative and overlook mis-assemblies.

Purpose of the Study:

To introduce REAPR, a novel tool for precise identification of errors in genome assemblies.
To enable quantitative comparison of multiple genome assemblies without a reference sequence.

Main Methods:

REAPR precisely identifies errors in genome assemblies.
Validation performed on complete genomes and de novo assemblies from various organisms (bacteria, malaria, C. elegans).

Main Results:

REAPR accurately assesses genome assembly accuracy.
Demonstrated that 86% of the human and 82% of the mouse reference genomes are error-free.
Provides corrected assembly statistics for quantitative comparison.

Conclusions:

REAPR offers a reliable method for assessing genome assembly accuracy.
Enables quantitative comparison of genome assemblies, improving ongoing genome projects.
The tool is publicly available for use in genomic research.