Error filtering, pair assembly and error correction for next-generation sequencing reads

Motivation: Next-generation sequencing produces vast amounts of data with errors that are difficult to distinguish from true biological variation when coverage is low. Results: We demonstrate large reductions in error frequencies, especially for high-error-rate reads, by three independent means: (i)...

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Bibliographic Details
Published inBioinformatics Vol. 31; no. 21; pp. 3476 - 3482
Main Authors Edgar, Robert C., Flyvbjerg, Henrik
Format Journal Article
LanguageEnglish
Published England 01.11.2015
Subjects
Algorithms
Assembly
Bioinformatics
Error correction
Filtering
Filtration
High-Throughput Nucleotide Sequencing - methods
Mathematical analysis
Packages
Sequencing
Software
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Summary:Motivation: Next-generation sequencing produces vast amounts of data with errors that are difficult to distinguish from true biological variation when coverage is low. Results: We demonstrate large reductions in error frequencies, especially for high-error-rate reads, by three independent means: (i) filtering reads according to their expected number of errors, (ii) assembling overlapping read pairs and (iii) for amplicon reads, by exploiting unique sequence abundances to perform error correction. We also show that most published paired read assemblers calculate incorrect posterior quality scores. Availability and implementation: These methods are implemented in the USEARCH package. Binaries are freely available at http://drive5.com/usearch. Contact:  robert@drive5.com Supplementary information: Supplementary data are available at Bioinformatics online.
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ISSN:1367-4803
1367-4811
1367-4811
1460-2059
DOI:10.1093/bioinformatics/btv401