FOCUS2: agile and sensitive classification of metagenomics data using a reduced database

Abstract

SummaryMetagenomics approaches rely on identifying the presence of organisms in the microbial community from a set of unknown DNA sequences. Sequence classification has valuable applications in multiple important areas of medical and environmental research. Here we introduce FOCUS2, an update of the previously published computational method FOCUS. FOCUS2 was tested with 10 simulated and 543 real metagenomes demonstrating that the program is more sensitive, faster, and more computationally efficient than existing methods.\n\nAvailabilityThe Python implementation is freely available at https://edwards.sdsu.edu/FOCUS2.\n\nSupplementary informationavailable at Bioinformatics online.