In metagenomics not only a single type of microorganism is studied, but the sequence information of the total community within an environmental sample. Consequently, over the past years an increasing focus has being laid on cultivation-independent methodologies such as metagenomics and single cell genomics approaches to discover and study microorganisms. The missing genomic data of millions of prokaryotes (“microbial dark matter”) obscures our knowledge of microbial diversity, metabolic potentials and evolutionary histories. ![]() In addition to technical challenges in cultivation, it has become increasingly apparent that many model microorganisms that have been cultivated and studied in the laboratory lost important (eco)physiological properties due to adaptive evolution to the applied conditions. Consequently, classical genome sequencing has been inaccessible for the vast majority of bacterial and archaeal species. Others grow so slowly, that it can take months or even years to obtain sufficient biomass for genomic analysis. It is estimated that over 99% of all environmental microorganisms remain uncultivatable under current laboratory conditions. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.ĭata Availability: The processed read datasets and scaffolds are available at MG-RAST under the project accession number 16910 as well as NCBI under the accession numbers SRR5035895 and SRR5035371.įunding: The authors received no specific funding for this work.Ĭompeting interests: The authors have declared that no competing interests exist. Received: ApAccepted: DecemPublished: January 18, 2017Ĭopyright: © 2017 Vollmers et al. In addition, we present detailed descriptions of the underlying principles and pitfalls of publically available assembly tools from a microbiologist’s perspective, and provide guidance regarding the user-friendliness, sensitivity and reliability of the resulting phylogenetic profiles.Ĭitation: Vollmers J, Wiegand S, Kaster A-K (2017) Comparing and Evaluating Metagenome Assembly Tools from a Microbiologist’s Perspective - Not Only Size Matters! PLoS ONE 12(1):Įditor: Francisco Rodriguez-Valera, Universidad Miguel Hernandez de Elche, SPAIN Our observations clearly demonstrate that different assembly tools can prove optimal, depending on the sample type, available computational resources and, most importantly, the specific research goal. In contrast to the highly anticipated "Critical Assessment of Metagenomic Interpretation" (CAMI) challenge, which uses general mock community-based assembler comparison we here tested assemblers on real Illumina metagenome sequencing data from natural communities of varying complexity sampled from forest soil and algal biofilms. In order to provide a comprehensive overview and guide for the microbiological scientific community, we assessed the most common and freely available metagenome assembly tools with respect to their output statistics, their sensitivity for low abundant community members and variability in resulting community profiles as well as their ease-of-use. Nevertheless, choosing the most appropriate methods for answering specific biological questions can be rather challenging, especially for non-bioinformaticians. Fortunately, a large diversity of specialized software tools is nowadays available. ![]() Limiting factors are partly the availability of computational resources, but mainly the bioinformatics expertise in establishing and applying appropriate processing and analysis pipelines. The production of data has dramatically increased over the past years and processing and analysis steps are becoming more and more of a bottleneck. With the constant improvement in cost-efficiency and quality of Next Generation Sequencing technologies, shotgun-sequencing approaches -such as metagenomics- have nowadays become the methods of choice for studying and classifying microorganisms from various habitats.
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