PlasClass

PlasClass classifies DNA sequences as plasmid or chromosomal to distinguish plasmid-derived contigs from chromosomal contigs in metagenomic and isolate assemblies.

Key Features:

• Accuracy for Short Sequences: Classifies shorter sequences typical of assembly contigs to improve reliability on fragmented assemblies.
• Comprehensive Training Dataset: Uses a current and extensive set of known plasmid sequences stratified by sequence length to support performance across lengths.
• Efficiency in Resource Utilization: Demonstrates improved accuracy and reduced time and memory requirements compared with existing tools.

Scientific Applications:

• Metagenomic Assemblies: Classifies contigs of uncertain origin in metagenomic datasets to support analyses of microbial community plasmid content.
• Isolate Assemblies: Identifies plasmid sequences within bacterial isolate assemblies to aid characterization of genome architecture and mobile elements.

Methodology:

Employs standard classifiers trained on the latest known plasmid sequences, with training stratified by sequence length.