plASgraph2: using graph neural networks to detect plasmid contigs from an assembly graph

plASgraph2: using graph neural networks to detect plasmid contigs from an assembly graph

Identification of plasmids from sequencing data is an important and challenging problem related to antimicrobial resistance spread and other One-Health issues. We provide a new architecture for identifying plasmid contigs in fragmented genome assemblies built from short-read data. We employ graph ne...

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Bibliographic Details
Main Authors: Janik Sielemann, Katharina Sielemann, Broňa Brejová, Tomáš Vinař, Cedric Chauve
Format: Article
Language:English
Published: Frontiers Media S.A. 2023-10-01
Series:Frontiers in Microbiology
Subjects:
bioinformatics
machine learning (ML)
classification
plasmids
assembly graph
Online Access:https://www.frontiersin.org/articles/10.3389/fmicb.2023.1267695/full

Internet

https://www.frontiersin.org/articles/10.3389/fmicb.2023.1267695/full

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