title: Karect: accurate correction of substitution, insertion and deletion errors for next-generation sequencing data.
abstract: BACKGROUND
  Next-generation sequencing generates large amounts of data affected by errors in the form of substitutions, insertions or deletions of bases. Error correction based on the high-coverage information, typically improves de novo assembly. Most existing tools can correct substitution errors only; some support insertions and deletions, but accuracy in many cases is low.
  
  
  RESULTS
  We present Karect, a novel error correction technique based on multiple alignment. Our approach supports substitution, insertion and deletion errors. It can handle non-uniform coverage as well as moderately covered areas of the sequenced genome. Experiments with data from Illumina, 454 FLX and Ion Torrent sequencing machines demonstrate that Karect is more accurate than previous methods, both in terms of correcting individual-bases errors (up to 10% increase in accuracy gain) and post de novo assembly quality (up to 10% increase in NGA50). We also introduce an improved framework for evaluating the quality of error correction.
  
  
  METHODS
  Karect is available at: http://aminallam.github.io/karect.
  
  
  BACKGROUND
  amin.allam@kaust.edu.sa
  
  
  BACKGROUND
  Supplementary data are available at Bioinformatics online.
authors.affiliation: Computer, Electrical and Mathematical Sciences and Engineering Division (CEMSE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia.
authors.forename: Amin
authors.initials: A
authors.lastname: Allam
authors.affiliation: Computer, Electrical and Mathematical Sciences and Engineering Division (CEMSE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia.
authors.forename: Panos
authors.initials: P
authors.lastname: Kalnis
authors.affiliation: Computer, Electrical and Mathematical Sciences and Engineering Division (CEMSE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia.
authors.forename: Victor
authors.initials: V
authors.lastname: Solovyev
mesh_terms: D000465:Algorithms; D002874:Chromosome Mapping; D019295:Computational Biology / Q000379:methods; D015894:Genome, Human; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D054643:INDEL Mutation / Q000235:genetics*; D016254:Mutagenesis, Insertional / Q000235:genetics*; D017422:Sequence Analysis, DNA / Q000379:methods*; D017384:Sequence Deletion