Question Regarding Plasmid Copy Number Calculation

[cici-Jing]

I am currently working with a metagenomic sample and I have both total DNA and total plasmid samples sequenced using Illumina. In addition, only the total plasmid sample was also sequenced with Nanopore long reads. I came across your tool, plassembler, which can calculate plasmid copy number, and I wanted to ask if it would be suitable to use plassembler for calculating plasmid copy number in my case.

Specifically, the data I have is as follows:

Total DNA and total plasmid samples sequenced using Illumina
Only the total plasmid sample sequenced with Nanopore long reads

I appreciate your help and insights!

[gbouras13]

Hi @songjing99 ,

In this case - I don't think so!

You cannot use the nanopore reads for copy number estimation as you don't have the underlying DNA for that.

My question is I guess, what does copy number mean in the metagenomic context? It only really makes sense for isolates I think. What would your plan be to run plassembler? It relies on assembling chromosome(s) so any copy number estimation would be vs those chromosomes. And with only short-reads for the chromosomes, plassembler might struggle here, as you don't have long reads to assemble the chromosomes into continuous genomes.

George