title: Pollux: platform independent error correction of single and mixed genomes.
abstract: 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.
authors.affiliation: David R. Cheriton School of Computer Science, University of Waterloo, 200 University Ave W, Waterloo, ON N2L 3G1, Canada. eric.marinier@uwaterloo.ca.
authors.forename: Eric
authors.initials: E
authors.lastname: Marinier
authors.affiliation: David R. Cheriton School of Computer Science, University of Waterloo, 200 University Ave W, Waterloo, ON N2L 3G1, Canada. dan.brown@uwaterloo.ca.
authors.forename: Daniel G
authors.initials: DG
authors.lastname: Brown
authors.affiliation: Department of Biology, University of Waterloo, 200 University Ave W, N2L3G1 Waterloo, Canada. mcconkey@uwaterloo.ca.
authors.forename: Brendan J
authors.initials: BJ
authors.lastname: McConkey
mesh_terms: D000465:Algorithms; D001419:Bacteria / Q000145:classification / Q000235:genetics*; D019295:Computational Biology; D004269:DNA, Bacterial / Q000032:analysis; D030541:Databases, Genetic; D016680:Genome, Bacterial; D059014:High-Throughput Nucleotide Sequencing / Q000295:instrumentation*; D017422:Sequence Analysis, DNA / Q000295:instrumentation* / Q000379:methods*; D012984:Software
chemical_list: D004269:DNA, Bacterial