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Summary: Longer sequencing reads, with at least 200 bases per template arenow common. While traditional aligners have adopted new strategies to improvethe mapping of longer reads, aligners specific to bisulfite-sequencing wereoptimized when much shorter reads were the norm. We sought to perform the firstcomparison using longer reads to determine which aligners were most accurateand efficient and to evaluate a novel software tool, bwa-meth, built on atraditional mapper that supports insertions, deletions and clipped alignments.We gauge accuracy by comparing the number of on and off-target reads from atargeted sequencing project and by simulations. Availability andImplementation: The benchmarking scripts and the bwa-meth software areavailable at https://github/com/brentp/bwa-meth/ under the MIT License.

Fast and accurate alignment of long bisulfite-seq reads