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This Week in Nucleic Acids Research: Aug 5, 2015

Researchers from Singapore introduce an algorithm called BatAlign that's intended to boost read alignment accuracy across parts of the genome with structural variations using a combination of reverse alignment and deep scanning strategies. The team tested the method using both simulated and real datasets, demonstrating that it could successfully align high-throughput sequencing reads containing small insertions and deletions, larger structural variant breakpoints, and other polymorphisms.

An Emory University team describes a statistical strategy dubbed "Dispersion Shrinkage for Sequencing Data with Single Replicates" (DSS-single) for finding differentially methylated regions using a single set of whole-genome bisulfite sequencing reads rather than replicate datasets. The strategy hinges on finding these differentially methylated regions based on patterns at nearby sequences where cytosine and guanine bases are abundant, the researchers say. Their DSS-single analyses of bisulfite sequencing data on simulated and cell line samples indicates that the approach "provides greater sensitivity, accuracy, and biological plausibility compared with existing methods."

Finally, a pair of researchers from the University of Oxford outlines a new scheme for doing multiplexed targeted enrichment on libraries prepared for sequencing on the Oxford Nanopore Technologies MinIon sequencing instrument. The approach involves generating bait sequences by PCR, the team says. These baits are then biotinylated before being used to enrich for specific target sequences. In addition to validating this method to enrich and pool libraries of Escherichia coli and the phage lambda, the investigators started teasing apart ideal bait sizes for large fragment libraries.