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Nat Methods. 2008 Aug;5(8):679-82. doi: 10.1038/nmeth.1230. Epub 2008 Jul 6.

Alta-Cyclic: a self-optimizing base caller for next-generation sequencing.

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  • 1Watson School of Biological Sciences, 1 Bungtown Road, Cold Spring Harbor, New York 11724, USA.

Abstract

Next-generation sequencing is limited to short read lengths and by high error rates. We systematically analyzed sources of noise in the Illumina Genome Analyzer that contribute to these high error rates and developed a base caller, Alta-Cyclic, that uses machine learning to compensate for noise factors. Alta-Cyclic substantially improved the number of accurate reads for sequencing runs up to 78 bases and reduced systematic biases, facilitating confident identification of sequence variants.

PMID:
18604217
PMCID:
PMC2978646
DOI:
10.1038/nmeth.1230
[PubMed - indexed for MEDLINE]
Free PMC Article
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