Journal
NUCLEIC ACIDS RESEARCH
Volume 32, Issue 2, Pages 562-569Publisher
OXFORD UNIV PRESS
DOI: 10.1093/nar/gkh216
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Funding
- NIAID NIH HHS [N01AI15447] Funding Source: Medline
- NLM NIH HHS [R01 LM006845, R01-LM06845] Funding Source: Medline
- NATIONAL LIBRARY OF MEDICINE [R01LM006845] Funding Source: NIH RePORTER
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By using information from an assembly of a genome, a new program called AutoEditor significantly improves base calling accuracy over that achieved by previous algorithms. This in turn improves the overall accuracy of genome sequences and facilitates the use of these sequences for polymorphism discovery. We describe the algorithm and its application in a large set of recent genome sequencing projects. The number of erroneous base calls in these projects was reduced by 80%. In an analysis of over one million corrections, we found that AutoEditor made just one error per 8828 corrections. By substantially increasing the accuracy of base calling, AutoEditor can dramatically accelerate the process of finishing genomes, which involves closing all gaps and ensuring minimum quality standards for the final sequence. It also greatly improves our ability to discover single nucleotide polymorphisms (SNPs) between closely related strains and isolates of the same species.
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