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The increase in available sequence data has advanced the field of microbiology; however, making sense of these data without bioinformatics skills is still problematic. We describe MICRA, an automatic pipeline, available as a web interface, for microbial identification and characterization through reads analysis. MICRA uses iterative mapping against reference genomes to identify genes and variations. Additional modules allow prediction of antibiotic susceptibility and resistance and comparing the results of several samples. MICRA is fast, producing few false-positive annotations and variant calls compared to current methods, making it a tool of great interest for fully exploiting sequencing data.   Electronic supplementary material  The online version of this article (doi:10.1186/s13059-017-1367-z) contains supplementary material, which is available to authorized users.

MICRA: an automatic pipeline for fast characterization of microbial genomes from high-throughput sequencing data