Dear SEA PHAGES,

Thousand thanks for support with a few URGENT questions.

1. Once you have the raw files generated from Illumina, do you first use fastQC to quality-control them, then use fastP to clean them, before using Newbler at all? If not, how do you quality-check and clean them before ever using Newbler or Consed?

2. I suspect the fastq files of my phage genomes are contaminated with bacterial reads. Would that be an issue when assembling the phage reads in Newbler? If it would, how might I filter out those unwanted contaminant reads? I couldn’t a tutorial or instructions manual on the matter, but if you have any, please feel free to point them to me.
Edited 15 Jul, 2023 13:57