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PMID: 18604217 Published · ppublish English Journal Article Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, Non-P.H.S.

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

Nature methods ·Vol. 5 ·No. 8 ·2008-08-00 ·Pages 679-82

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

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.

MeSH Terms
Animals Databases, Nucleic Acid Humans Research Design Sensitivity and Specificity Sequence Analysis, DNA/methods,standards Software
Authors & Affiliations
5 authors, click to expand affiliations / ORCID
Erlich Yaniv
Watson School of Biological Sciences, 1 Bungtown Road, Cold Spring Harbor, New York 11724, USA.
Mitra Partha P
delaBastide Melissa
McCombie W Richard
Hannon Gregory J
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Article Info
Journal
Nature methods
Abbr.
Nat Methods
ISSN
1548-7105
DOI
10.1038/nmeth.1230
Published
2008-08-00
Epub
2008-00-06
Pages
679-82
Language
English
Region
United States
NLM ID
101215604
PMCID
PMC2978646
Subset
IM
Grants
NCI NIH HHS · P01 CA013106 · United States
NCI NIH HHS · P01 CA013106-37 · United States
NCI NIH HHS · P01 CA013106-38 · United States
Howard Hughes Medical Institute · United States
External Links
PubMed source DOI: 10.1038/nmeth.1230 PMC Full Text View journal details
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