Dataset Information

ReviSTER: an automated pipeline to revise misaligned reads to simple tandem repeats.

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.

Availability

ReviSTER is open-source software available at http://revister.sourceforge.net.

Contact

garner@vbi.vt.edu

Supplementary information

Supplementary data are available at Bioinformatics online.

SUBMITTER: Tae H

PROVIDER: S-EPMC3702252 | biostudies-literature | 2013 Jul

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

ReviSTER: an automated pipeline to revise misaligned reads to simple tandem repeats.

Tae Hongseok H McMahon Kevin W KW Settlage Robert E RE Bavarva Jasmin H JH Garner Harold R HR

Bioinformatics (Oxford, England) 20130515 14

<h4>Motivation</h4>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 sequ ...[more]

PMID: 23677944

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Dataset Information

ReviSTER: an automated pipeline to revise misaligned reads to simple tandem repeats.

Motivation

Results

Availability

Contact

Supplementary information

Publications

ReviSTER: an automated pipeline to revise misaligned reads to simple tandem repeats.

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