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

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Abstract
A new base caller for the Illumina Genome Analyzer uses machine learning to compensate for noise factors and improves accuracy for up to 78-base-pair sequencing reads. 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.