MMR

The MMR (multi-mapper resolution) tool is a software designed to improve the mapping of high-throughput sequencing data to a reference genome, by inferring optimal mapping locations from the coverage density of other mapped reads. By filtering alignments with MMR, the accuracy of downstream analyses, such as transcript quantification and differential testing, can be significantly improved, and the alignment file sizes can be reduced by more than 50%. The MMR algorithm can be easily applied as a post-processing step to existing alignment files in BAM format and is available as open-source code and documentation for download.