Journal
BIOINFORMATICS
Volume 27, Issue 19, Pages 2756-2757Publisher
OXFORD UNIV PRESS
DOI: 10.1093/bioinformatics/btr451
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Funding
- National Science Foundation [ER 0949453]
- Direct For Biological Sciences [0949453] Funding Source: National Science Foundation
- Emerging Frontiers [0949453] Funding Source: National Science Foundation
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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.
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