We present a fast and exact algorithm to compute the (k,e)-mappability. Its inverse, the (k,e)-frequency counts the number of occurrences of each k-mer with up to e errors in a sequence. The algorithm we present is a magnitude faster than the algorithm in the widely used GEM suite while not relying on heuristics, and can even compute the mappability for short k-mers on highly repetitive plant genomes. We also show that mappability can be computed on multiple sequences to identify marker genes illustrated by the example of E. coli strains. GenMap allows exporting the mappability information into different formats such as raw output, wig and bed-files. The application and its C++ source code is available on https://github.com/cpockrandt/genmap .
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