ReviSTER: An automated pipeline to revise misaligned reads to simple tandem repeats

Hongseok Tae, Kevin W. McMahon, Robert E. Settlage, Jasmin H. Bavarva, Harold R. Garner

Research output: Contribution to journalArticle

Abstract

Motivation: 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.

Original languageEnglish (US)
Pages (from-to)1734-1741
Number of pages8
JournalBioinformatics
Volume29
Issue number14
DOIs
StatePublished - Jul 15 2013

ASJC Scopus subject areas

  • Statistics and Probability
  • Biochemistry
  • Molecular Biology
  • Computer Science Applications
  • Computational Theory and Mathematics
  • Computational Mathematics

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    Tae, H., McMahon, K. W., Settlage, R. E., Bavarva, J. H., & Garner, H. R. (2013). ReviSTER: An automated pipeline to revise misaligned reads to simple tandem repeats. Bioinformatics, 29(14), 1734-1741. https://doi.org/10.1093/bioinformatics/btt277