Gleb Goussarov, Mohamed Mysara, Ilse Cleenwerck, Jürgen Claesen, Natalie Leys, Peter Vandamme, Rob Van Houdt
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引用次数: 0
Abstract
Metagenome community analyses, driven by the continued development in sequencing technology, is rapidly providing insights in many aspects of microbiology and becoming a cornerstone tool. Illumina, Oxford Nanopore Technologies (ONT) and Pacific Biosciences (PacBio) are the leading technologies, each with their own advantages and drawbacks. Illumina provides accurate reads at a low cost, but their length is too short to close bacterial genomes. Long reads overcome this limitation, but these technologies produce reads with lower accuracy (ONT) or with lower throughput (PacBio high-fidelity reads). In a critical first analysis step, reads are assembled to reconstruct genomes or individual genes within the community. However, to date, the performance of existing assemblers has never been challenged with a complex mock metagenome. Here, we evaluate the performance of current assemblers that use short, long or both read types on a complex mock metagenome consisting of 227 bacterial strains with varying degrees of relatedness. We show that many of the current assemblers are not suited to handle such a complex metagenome. In addition, hybrid assemblies do not fulfil their potential. We conclude that ONT reads assembled with CANU and Illumina reads assembled with SPAdes offer the best value for reconstructing genomes and individual genes of complex metagenomes, respectively.
期刊介绍:
We publish high-quality original research on bacteria, fungi, protists, archaea, algae, parasites and other microscopic life forms.
Topics include but are not limited to:
Antimicrobials and antimicrobial resistance
Bacteriology and parasitology
Biochemistry and biophysics
Biofilms and biological systems
Biotechnology and bioremediation
Cell biology and signalling
Chemical biology
Cross-disciplinary work
Ecology and environmental microbiology
Food microbiology
Genetics
Host–microbe interactions
Microbial methods and techniques
Microscopy and imaging
Omics, including genomics, proteomics and metabolomics
Physiology and metabolism
Systems biology and synthetic biology
The microbiome.