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1: Nat Methods. 2008 Aug;5(8):679-82. Epub 2008 Jul 6.
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Alta-Cyclic: a self-optimizing base caller for next-generation sequencing.

Erlich Y, Mitra PP, delaBastide M, McCombie WR, Hannon GJ.

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

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.

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PMID: 18604217 [PubMed - indexed for MEDLINE]