ReDis: efficient metagenomic profiling via assigning ambiguous reads

Metagenomic profiling is one of the primary means of microbiome analysis, which includes classification of sequencing reads and quantification of their relative abundances. Although many methods have been developed for metagenomic profiling, metagenomic profiling remains challenges on striking a delicate balance between accuracy and runtime as well as assigning the ambiguous reads. Here, we present a novel method, named ReDis, to overcome the above issues. ReDis combines Kraken2 with Minimap2 for aligning sequencing reads against a reference database with hundreds of gigabytes (GB) in size accurately within feasible time, and then uses a novel statistical model to assign the ambiguous reads for producing accurate abundance estimates. In contrast to the popular Kraken2+Bracken, ReDis improved the accuracy of abundance estimation on simulated reads from two highly similar genomes: Escherichia coli and Shigella flexneri.