bookmark MMR / MultiMapper Resolution A post-processor for BAM files, resolving ambiguous alignment locations. MMR infers optimal mapping locations from the coverage density of other mapped reads. Filtering alignments with MMR can significantly improve the performance of downstream analyses like transcript quantitation and differential testing. Our efficient implementation of the MMR algorithm is easily applicable as a post-processing step to existing alignment files in BAM format. Its complexity scales linearly with the number of alignments and requires no further inputs.