PLASMe: a tool to identify PLASMid contigs from short-read assemblies using transformer.Plasmids are mobile genetic elements that carry important accessory genes.  In this work, we develop a plasmid detection tool PLASMe that capitalizes on the strength of alignment and learning-based methods.  Closely related plasmids can be easily identified using the alignment component in PLASMe while diverged plasmids can be predicted using order-specific Transformer models.  We compared PLASMe and other tools on detecting complete plasmids, plasmid contigs, and contigs assembled from CAMI2 simulated data.  PLASMe achieved the highest F1-score.  After validating PLASMe on data with known labels, we also tested it on real metagenomic and plasmidome data.  The examination of some commonly used marker genes shows that PLASMe exhibits more reliable performance than other tools.
PLASMe
PLASMe: a tool to identify PLASMid contigs from short-read assemblies using transformer.Plasmids are mobile genetic elements that carry important accessory genes.  We compared PLASMe and other tools on detecting complete plasmids, plasmid contigs, and contigs assembled from CAMI2 simulated data. 
PLASMid contigs
PLASMe: a tool to identify PLASMid contigs from short-read assemblies using transformer.Plasmids are mobile genetic elements that carry important accessory genes. 
short-read assemblies
PLASMe: a tool to identify PLASMid contigs from short-read assemblies using transformer.Plasmids are mobile genetic elements that carry important accessory genes.  Closely related plasmids can be easily identified using the alignment component in PLASMe while diverged plasmids can be predicted using order-specific Transformer models.  By encoding plasmid sequences as a language defined on the protein cluster-based token set, Transformer can learn the importance of proteins and their correlation through positionally token embedding and the attention mechanism. 
transformer