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All posts created by jcaoyao@gmail.com
Link to this post | posted 15 Jul, 2023 13:55 | |
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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. |
Posted in: Newbler → Getting Started with Phage Assembly