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Genomics. 2013 Jul;102(1):35-7. doi: 10.1016/j.ygeno.2013.03.002. Epub 2013 Mar 29.

RF: a method for filtering short reads with tandem repeats for genome mapping.

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Research Program for Computational Science, Research and Development Group for Next-Generation Integrated Living Matter Simulation, Fusion of Data and Analysis Research and Development Team, RIKEN, Japan.


Next-generation sequencing platforms generate short (50-150bp) reads that can be mapped onto the reference genome. Repetitive sequences in the genome, because of the presence of similar or identical sequences, cause mapping errors in the case of the short reads. By filtering short reads with repeats, mapping will be improved. I developed RF. RF is a new method that filters short reads with tandem repeats. A scoring scheme was developed that assigned higher scores to regions with tandem repeats and lower scores to regions without tandem repeats. In this study, RF was applied to filter out short reads with repeats, before short reads were mapped onto the same genomic contig by using a short read-mapping program. The result suggests RF improved the proportion of correctly mapped short reads on filtering the repeats. RF is a useful tool for reducing mapping errors of short reads onto reference genomes.

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