Dataset Information

Mauve assembly metrics.

ABSTRACT:

Summary

High-throughput DNA sequencing technologies have spurred the development of numerous novel methods for genome assembly. With few exceptions, these algorithms are heuristic and require one or more parameters to be manually set by the user. One approach to parameter tuning involves assembling data from an organism with an available high-quality reference genome, and measuring assembly accuracy using some metrics. We developed a system to measure assembly quality under several scoring metrics, and to compare assembly quality across a variety of assemblers, sequence data types, and parameter choices. When used in conjunction with training data such as a high-quality reference genome and sequence reads from the same organism, our program can be used to manually identify an optimal sequencing and assembly strategy for de novo sequencing of related organisms.

Availability

GPL source code and a usage tutorial is at http://ngopt.googlecode.com

Contact

aarondarling@ucdavis.edu

Supplementary information

Supplementary data is available at Bioinformatics online.

SUBMITTER: Darling AE

PROVIDER: S-EPMC3179657 | biostudies-literature | 2011 Oct

REPOSITORIES: biostudies-literature

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Publications

Mauve assembly metrics.

Darling Aaron E AE Tritt Andrew A Eisen Jonathan A JA Facciotti Marc T MT

Bioinformatics (Oxford, England) 20110802 19

<h4>Summary</h4>High-throughput DNA sequencing technologies have spurred the development of numerous novel methods for genome assembly. With few exceptions, these algorithms are heuristic and require one or more parameters to be manually set by the user. One approach to parameter tuning involves assembling data from an organism with an available high-quality reference genome, and measuring assembly accuracy using some metrics. We developed a system to measure assembly quality under several scori ...[more]

PMID: 21810901

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Dataset Information

Mauve assembly metrics.

Summary

Availability

Contact

Supplementary information

Publications

Mauve assembly metrics.

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