Fig. 1

Overview of MetaPro workflow and performance relative to two state-or-the art pipelines. A Overview of MetaPro’s workflow, including the tools and databases used at each step. The bar on the right indicates the relative time required for each phase of the pipeline. B Chord diagrams tracking the trajectory of sequence reads across each pipeline, in comparison to MetaPro. Each arch represents one category of reads, bands mapping between arcs indicate the proportion of reads assigned by each pipeline to the associated category. C Stacked barcharts depicting the number of reads annotated to specific taxa in NOD mouse samples, and kimchi samples by BWA alignments, MetaPro, HUMAnN3, and SAMSA2. The NOD mouse datasets were generated from gut samples from mice inoculated with a defined microbial consortium (Altered Schaedler Flora (ASF) [29]. In addition to the 8 taxa associated with ASF, reads were also assigned to Parabacteroidesgoldsteinii, a close relative of Parabacteroides ASF519 (see legend). The kimchi datasets comprise five major taxa (see legend [30,31,32,33,34]). It should be noted that Leuconostoc gasicomitatum reported in the original publication is currently classified as a subspecies of Leuconostoc gelidum. For NOD sample SRR1828965, HUMAnN3 did not annotate any reads