CAMISIM 2.0 – Simulating metagenomes and microbial communities

Abstract. A lot of progress has been made in the field of metagenomics in the past couple of years, both in terms of computational methods as well as in experimental setup and sequencing technologies. Still, new laboratory protocols, sequencing chemistries and metagenomics software are being developed and published all the time. Thus, it is important for the community to keep being able to assess and compare all these different methods. For this, being able to easily and quickly simulate metagenomic datasets is key.

The first version of CAMISIM was published in 2019 and was widely adopted as a simulation software for microbial communities and metagenomes. It provided the benchmark datasets for the first and second CAMI challenges as well as datasets for dozens of other software methods. To keep up with the current developments, CAMISIM is under constant development and received multiple updates and new releases since 2019. Now, we present the 2.0 version of CAMISIM, which not only brings CAMISIM up to speed with the latest recommendations for software workflows from different initiatives, but also solves some longer standing issues, includes the latest sequencing simulators and offers more customisation and flexibility to the users, while an extension from only metagenomics to also metatranscriptomics datasets is on the horizon.

All versions of CAMISIM are freely available under the Apache 2.0 license under https://github.com/CAMI-challenge/CAMISIM