Running Phamb on long reads polished with short reads

[emilyjunkins]

Hello,

I have long read nanopore data assembled with flye and polished with illumina reads. Is phamb compatible with a long read assembler like flye?

[joacjo]

Hi Emily

Yes Phamb is compatible, I am assuming at this point you are binning the long-read assembled contigs. Even though we have not benchmarked this, I would think that long-read assembled contigs should improve both Viral-binning and prediction of viral bins. If you have no intention of running binning on your contigs to improve viral completeness and rescue viral fragmentation, I would short-cut to running CheckV or Vibrant on the long-read assembled contigs.

Best, Joachim