plasmid spades R1/R2 files?

Question

[sarah.goldstein]

Hello,

I know spades innately saves the corrected R1/R2 fastq files for the assembly. However, the plasmid spades program only uses a subset of those reads, so I was wondering if there is a flag or way to pull out just those reads used to build the plasmid assembly and place them in separate R1/R2 files?

I am also open to using other mapping methods (BWA) but I just don't know how to split fastq files into genomic and plasmid DNA.

Thanks!

[GenoMax]

If you have the genomic reference available you can use an aligner (look into bbmap.sh from BBMap suite with outu=file.fq.gz option) to collect reads that do not map. Those should be your plasmid reads (assuming there is no other entity expected to be present).