I am working with virus nanopore sequencing data. I have to remove host genome from the reads. I want to run the QC on the fastq file after host genome subtraction. I have used nanoplot. It is slow. I dont have summary.txt. Is there any nanopore read specific qc package which can directly take nanopore fastq files.

  • $\begingroup$ Oh yeh, NanoPlot can be pretty slow when you only have fastq data. I'm happy to look at contributions on how to make it faster. Do you have a machine with multiple cores? Because if your data is split across multiple fastq files then NanoPlot can read those in parallel. $\endgroup$ Jul 15 '20 at 18:47
  • $\begingroup$ I have 6 core with 12 threads. How can I split the fastq files and run them in parallel? $\endgroup$ Jul 19 '20 at 19:18
  • $\begingroup$ Splitting can be done e.g. with fastqsplitter.readthedocs.io/en/stable, or the Unix split tool. $\endgroup$ Jul 22 '20 at 9:01

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