title: Alta-Cyclic: a self-optimizing base caller for next-generation sequencing.
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.
authors.affiliation: Watson School of Biological Sciences, 1 Bungtown Road, Cold Spring Harbor, New York 11724, USA.
authors.forename: Yaniv
authors.initials: Y
authors.lastname: Erlich
authors.forename: Partha P
authors.initials: PP
authors.lastname: Mitra
authors.forename: Melissa
authors.initials: M
authors.lastname: delaBastide
authors.forename: W Richard
authors.initials: WR
authors.lastname: McCombie
authors.forename: Gregory J
authors.initials: GJ
authors.lastname: Hannon
mesh_terms: D000818:Animals; D030561:Databases, Nucleic Acid; D006801:Humans; D012107:Research Design; D012680:Sensitivity and Specificity; D017422:Sequence Analysis, DNA / Q000379:methods* / Q000592:standards; D012984:Software