Body: <p>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.</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-07-15T18:47:33.373Z
Comments.Text: 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.
Comments.UserDisplayName: Wouter De Coster
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-07-19T19:18:44.090Z
Comments.Text: I have 6 core with 12 threads. How can I split the fastq files and run them in parallel?
Comments.UserDisplayName: Arun Venugopalan
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-07-22T09:01:26.330Z
Comments.Text: Splitting can be done e.g. with https://fastqsplitter.readthedocs.io/en/stable/, or the Unix split tool.
Comments.UserDisplayName: Wouter De Coster
Tags: <fastq><nanopore><qc>
Title: nanopore QC measures on fastq file
ThreadText: # nanopore QC measures on fastq file
  
  (Asked by: username_0 on 2020-07-14)
  
  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.
  
  **Tags:** fastq, nanopore, qc
  
  > **Comments:**
  > **username_1**: 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.  
  > **username_0**: I have 6 core with 12 threads. How can I split the fastq files and run them in parallel?  
  > **username_1**: Splitting can be done e.g. with https://fastqsplitter.readthedocs.io/en/stable/, or the Unix split tool.  
  
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  ## 0 answers
  
  