Pollux: platform independent error correction of single and mixed genomes

Background Second-generation sequencers generate millions of relatively short, but error-prone, reads. These errors make sequence assembly and other downstream projects more challenging. Correcting these errors improves the quality of assemblies and projects which benefit from error-free reads. Resu...

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Vydáno v:BMC bioinformatics Ročník 16; číslo 1; s. 10
Hlavní autoři: Marinier, Eric, Brown, Daniel G, McConkey, Brendan J
Médium: Journal Article
Jazyk:angličtina
Vydáno: London BioMed Central 16.01.2015
BioMed Central Ltd
Témata:
Algorithms
Assembly
Bacteria - classification
Bacteria - genetics
Bioinformatics
Biomedical and Life Sciences
Computational Biology
Computational Biology/Bioinformatics
Computer Appl. in Life Sciences
Computer programs
Databases, Genetic
DNA, Bacterial - analysis
Error correction
Error detection
Genome, Bacterial
High-Throughput Nucleotide Sequencing - instrumentation
Life Sciences
Microarrays
Platforms
Sequence Analysis, DNA - instrumentation
Sequence Analysis, DNA - methods
Sequencing
Software
Torrents
Assembly
Next-generation sequencing
Error correction
ISSN:1471-2105, 1471-2105
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Shrnutí:Background Second-generation sequencers generate millions of relatively short, but error-prone, reads. These errors make sequence assembly and other downstream projects more challenging. Correcting these errors improves the quality of assemblies and projects which benefit from error-free reads. Results We have developed a general-purpose error corrector that corrects errors introduced by Illumina, Ion Torrent, and Roche 454 sequencing technologies and can be applied to single- or mixed-genome data. In addition to correcting substitution errors, we locate and correct insertion, deletion, and homopolymer errors while remaining sensitive to low coverage areas of sequencing projects. Using published data sets, we correct 94% of Illumina MiSeq errors, 88% of Ion Torrent PGM errors, 85% of Roche 454 GS Junior errors. Introduced errors are 20 to 70 times more rare than successfully corrected errors. Furthermore, we show that the quality of assemblies improves when reads are corrected by our software. Conclusions Pollux is highly effective at correcting errors across platforms, and is consistently able to perform as well or better than currently available error correction software. Pollux provides general-purpose error correction and may be used in applications with or without assembly.
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ISSN:1471-2105
1471-2105
DOI:10.1186/s12859-014-0435-6