The Genome Multitool (GEM) mapper rapidly and accurately provides all alignments of a read within a user-defined number of mismatches.
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Faust, G., Hall, I. GEM: crystal-clear DNA alignment. Nat Methods 9, 1159–1160 (2012). https://doi.org/10.1038/nmeth.2256
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DOI: https://doi.org/10.1038/nmeth.2256