Method

1. Long reads are filtered using chopper.
2. Long-read only assembly is conducted with Flye or optionally Raven if --use_raven is specified.
3. If the resulting assembly is checked. Contigs bigger than the provided chromosome size -c, are identified as chromosomal and extracted. Any other contigs are extracted as putative plasmid contigs, if Flye assembled any. If no contigs were larger than -c, plassembler will exit - you probably need to get some more long reads to complete your assembly (or check -c wasn't too big).
4. Short reads are filtered using fastp.
5. Long and short reads are mapped to a reference containing the chromosomal contigs plus putative plasmid contigs using minimap2.
6. All reads that map to the putative plasmid contigs and all reads that are unmapped are extracted and combined.
7. These reads are assembled using the hybrid assembler Unicycler to generate final plasmid contigs.
8. Average read coverage depth for each plasmid is calculated using a modified version of code found here. See also this paper.
9. Plasmid copy number is calculated by dividing the plasmid read depth by the chromosome read depth.
10. All plasmid contigs are compared against PLSDB using mash with a cutoff maximum mash distance of 0.1.