Dataset Information

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 assemblers, 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/.

Supplementary information

Supplementary data are available at Bioinformatics online.

SUBMITTER: David L

PROVIDER: S-EPMC7332565 | biostudies-literature | 2020 Jul

REPOSITORIES: biostudies-literature

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Publications

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

David Laurent L Vicedomini Riccardo R Richard Hugues H Carbone Alessandra A

Bioinformatics (Oxford, England) 20200701 13

<h4>Motivation</h4>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.<h4>Results</h4>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 ...[more]

PMID: 32330240

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Dataset Information

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

Motivation

Results

Availability and implementation

Supplementary information

Publications

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

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