KrakenUniq: confident and fast metagenomics classification using unique k-mer counts

KrakenUniq: confident and fast metagenomics classification using unique k-mer counts

F. P. Breitwieser, D. N. Baker, S. L. Salzberg

Abstract False-positive identifications are a significant problem in metagenomics classification. We present KrakenUniq, a novel metagenomics classifier that combines the fast k-mer-based classification of Kraken with an efficient algorithm for assessing the coverage of unique k-mers found in each species in a dataset. On various test datasets, KrakenUniq gives better recall and precision than other methods and effectively classifies and distinguishes pathogens with low abundance from false positives in infectious disease samples. By using the probabilistic cardinality estimator HyperLogLog, KrakenUniq runs as fast as Kraken and requires little additional memory. KrakenUniq is freely available at https://github.com/fbreitwieser/krakenuniq.

2018

metagenomics, Microbiome, Metagenomics classification, Pathogen Detection, Infectious disease diagnosis

DOI: 10.1186/s13059-018-1568-0

Genome Biology

BMC

Biology (General), Genetics

EN