deSPI: efficient classification of metagenomic reads with lightweight de Bruijn graph-based reference indexing

Summary In metagenomic studies, fast and effective tools are on wide demand to implement taxonomy classification for upto billions of reads. Herein, we propose deSPI, a novel read classification method that classifies reads by recognizing and analyzing the matches between reads and reference with de Bruijn graph-based lightweight reference indexing. deSPI has faster speed with relatively small memory footprint, meanwhile, it can also achieve higher or similar sensitivity and accuracy. Availability the C++ source code of deSPI is available at https://github.com/hitbc/deSPI Contact ydwang@hit.edu.cn Supplementary information Supplementary data are available at Bioinformatics online.