Alta-Cyclic: a self-optimizing base caller for next-generation sequencing.
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.
Erlich
Yaniv
Y
Watson School of Biological Sciences, 1 Bungtown Road, Cold Spring Harbor, New York 11724, USA.
Mitra
Partha P
PP
delaBastide
Melissa
M
McCombie
W Richard
WR
Hannon
Gregory J
GJ
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