Dataset Information

AMAISE: a machine learning approach to index-free sequence enrichment.

ABSTRACT: Metagenomics holds potential to improve clinical diagnostics of infectious diseases, but DNA from clinical specimens is often dominated by host-derived sequences. To address this, researchers employ host-depletion methods. Laboratory-based host-depletion methods, however, are costly in terms of time and effort, while computational host-depletion methods rely on memory-intensive reference index databases and struggle to accurately classify noisy sequence data. To solve these challenges, we propose an index-free tool, AMAISE (A Machine Learning Approach to Index-Free Sequence Enrichment). Applied to the task of separating host from microbial reads, AMAISE achieves over 98% accuracy. Applied prior to metagenomic classification, AMAISE results in a 14-18% decrease in memory usage compared to using metagenomic classification alone. Our results show that a reference-independent machine learning approach to host depletion allows for accurate and efficient sequence detection.

SUBMITTER: Krishnamoorthy M

PROVIDER: S-EPMC9184628 | biostudies-literature | 2022 Jun

REPOSITORIES: biostudies-literature

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AMAISE: a machine learning approach to index-free sequence enrichment.

Krishnamoorthy Meera M Ranjan Piyush P Erb-Downward John R JR Dickson Robert P RP Wiens Jenna J

Communications biology 20220609 1

Metagenomics holds potential to improve clinical diagnostics of infectious diseases, but DNA from clinical specimens is often dominated by host-derived sequences. To address this, researchers employ host-depletion methods. Laboratory-based host-depletion methods, however, are costly in terms of time and effort, while computational host-depletion methods rely on memory-intensive reference index databases and struggle to accurately classify noisy sequence data. To solve these challenges, we propos ...[more]

PMID: 35681015

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AMAISE: a machine learning approach to index-free sequence enrichment.

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AMAISE: a machine learning approach to index-free sequence enrichment.

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