Simulating Illumina Metagenomic Data with InSilicoSeq

Hadrien Gourlé, Oskar Karlsson-Lindsjö, Juliette Hayer, Erik Bongcam-Rudloff


Motivation: The accurate in-silico simulation of metagenomic datasets is of great importance for benchmarking bioinformatics tools as well as for experimental design. Users are dependant on large-scale simulation to not only design experiments and new projects but also for accurate estimation of computational needs within a project. Unfortunately, most current read simulators are either not suited for metagenomics, out of date or relatively poorly documented. In this article, we describe InSilicoSeq, a software package to simulate metagenomic Illumina sequencing data. InsilicoSeq has a simple command-line interface and extensive documentation.
Results: InSilicoSeq is implemented in Python and capable of simulating realistic Illumina (meta) genomic data in a parallel fashion with sensible default parameters.
Availability: Source code and documentation are available under the MIT license at and

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