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Targeted domain assembly for fast functional profiling of metagenomic datasets with S3A

Abstract : Motivation: The understanding of the ever-increasing number of metagenomic sequences accumulating in our databases demands for approaches that rapidly 'explore' the content of multiple and/or large metagenomic datasets with respect to specific domain targets, avoiding full domain annotation and full assembly. Results: S3A is a fast and accurate domain-targeted assembler designed for a rapid functional profiling. It is based on a novel construction and a fast traversal of the Overlap-Layout-Consensus graph, designed to reconstruct coding regions from domain annotated metagenomic sequence reads. S3A relies on high-quality domain annotation to efficiently assemble metagenomic sequences and on the design of a new confidence measure for a fast evaluation of overlapping reads. Its implementation is highly generic and can be applied to any arbitrary type of annotation. On simulated data, S3A achieves a level of accuracy similar to that of classical metagenomics assembly tools while permitting to conduct a faster and sensitive profiling on domains of interest. When studying a few dozens of functional domains-a typical scenario-S3A is up to an order of magnitude faster than general purpose metagenomic assem-blers, thus enabling the analysis of a larger number of datasets in the same amount of time. S3A opens new avenues to the fast exploration of the rapidly increasing number of metagenomic datasets displaying an ever-increasing size. Availability and implementation: S3A is available at http://www.lcqb.upmc.fr/S3A_ASSEMBLER/.
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Laurent David, Riccardo Vicedomini, Hugues Richard, Alessandra Carbone. Targeted domain assembly for fast functional profiling of metagenomic datasets with S3A. Bioinformatics, Oxford University Press (OUP), 2020, 36 (13), pp.3975-3981. ⟨10.1093/bioinformatics/btaa272⟩. ⟨hal-02935519⟩

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