%0 Journal Article %A João F Matias Rodrigues %A Thomas SB Schmidt %A Janko Tackmann %A Christian von Mering %T MAPseq: improved speed, accuracy and consistency in ribosomal RNA sequence analysis %D 2017 %R 10.1101/126953 %J bioRxiv %P 126953 %X Metagenomic sequencing has become crucial to studying microbial communities, but meaningful taxonomic analysis and inter-comparison of such data are still hampered by technical limitations, between-study design variability and inconsistencies between taxonomies used. Here we present MAPseq, a framework for reference-based rRNA metagenomic analysis that is up to 30% more accurate (F1/2 score) and up to one hundred times faster than existing solutions, providing in a single run multiple taxonomy classifications and hierarchical OTU mappings, for both amplicon and shotgun sequencing strategies, and for datasets of virtually any size. Availability: Source code and binaries are freely available at http://meringlab.org/software/mapseq/ %U https://www.biorxiv.org/content/biorxiv/early/2017/04/12/126953.full.pdf