Dataset encompassing: The recovered MAGs by 6 different metagenomics pipelines (ATLAS, DATMA, MetaWRAP, MUFFIN, nf-core/mag and SnakeMAGs) using a mock community as input (SRR8359173 and SRR9328980), complemented with the output from MAGFlow (v1.0.0) using these MAGs as input for their quality assessment and taxonomical annotation. The MAGs produced by nf-core/mag using rice/rhizosphere sequenced libraries (PRJNA663614, PRJNA448773 and PRJNA645385) in either single assembly/single binning or co-assembly/co-binning mode, complemented with the output from MAGFlow (v1.0.0) using these MAGs as input for their quality assessment and taxonomical annotation. Scripts, commands and configuration files to run the different pipelines (ATLAS, DATMA, MetaWRAP, MUFFIN, nf-core/mag and SnakeMAGs) and reproduce the experimental conditions. Outputs, commands and scripts to run Metabinner and Semibin in their default configuration using the rice soil samples co-assembly, along with the MAGFlow (v1.1.0) output to compare these binners against MetaBAT2.