title: ReviSTER: an automated pipeline to revise misaligned reads to simple tandem repeats.
abstract: BACKGROUND
  Simple tandem repeats are highly variable genetic elements and widespread in genomes of many organisms. Next-generation sequencing technologies have enabled a robust comparison of large numbers of simple tandem repeat loci; however, analysis of their variation using traditional sequence analysis approaches still remains limiting and problematic due to variants occurring in repeat sequences confusing alignment programs into mapping sequence reads to incorrect loci when the sequence reads are significantly different from the reference sequence.
  
  
  RESULTS
  We have developed a program, ReviSTER, which is an automated pipeline using a 'local mapping reference reconstruction method' to revise mismapped or partially misaligned reads at simple tandem repeat loci. RevisSTER estimates alleles of repeat loci using a local alignment method and creates temporary local mapping reference sequences, and finally remaps reads to the local mapping references. Using this approach, ReviSTER was able to successfully revise reads misaligned to repeat loci from both simulated data and real data.
  
  
  BACKGROUND
  ReviSTER is open-source software available at http://revister.sourceforge.net.
  
  
  BACKGROUND
  garner@vbi.vt.edu
  
  
  BACKGROUND
  Supplementary data are available at Bioinformatics online.
authors.affiliation: Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, VA 24061, USA.
authors.forename: Hongseok
authors.initials: H
authors.lastname: Tae
authors.forename: Kevin W
authors.initials: KW
authors.lastname: McMahon
authors.forename: Robert E
authors.initials: RE
authors.lastname: Settlage
authors.forename: Jasmin H
authors.initials: JH
authors.lastname: Bavarva
authors.forename: Harold R
authors.initials: HR
authors.lastname: Garner
mesh_terms: D000483:Alleles; D059472:Exome; D023281:Genomics; D060005:Genotyping Techniques; D006238:Haploidy; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D016415:Sequence Alignment / Q000379:methods*; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software; D020080:Tandem Repeat Sequences