Fig. 1

UML diagram of the CAMISIM workflow. CAMISIM starts with the “community design” step, which can either be de novo, requiring a taxon mapping file and reference genomes or based on a taxonomic profile. This step produces a community genome and taxon profile which is used for the metagenome simulation using one of currently four read simulators (ART, wgsim, PBsim, NanoSim). The resulting reads and bam-files mapping the reads to the original genomes are used to create the gold standards before all the files can be anonymized and shuffled in the post-processing step