<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>

CC BY-SA 4.0
2020-07-15T18:47:33.373Z
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.
Wouter De Coster
CC BY-SA 4.0
2020-07-19T19:18:44.090Z
I have 6 core with 12 threads. How can I split the fastq files and run them in parallel?
Arun Venugopalan
CC BY-SA 4.0
2020-07-22T09:01:26.330Z
Splitting can be done e.g. with https://fastqsplitter.readthedocs.io/en/stable/, or the Unix split tool.
Wouter De Coster
<fastq><nanopore><qc>
nanopore QC measures on fastq file
# 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

