Body: <p>I am new in bioinformatic field. I would like to know a way to generate a consensus sequence from nanopore fastq files (fastq files demultiplexed).</p>
  <p>I usually generate a consensus sequence with &quot;MEDAKA&quot; of artic protocol, but it is used to generate a SARS CoV 2 sequence only.</p>
  <p>I would like to know a differente way to do it with another program, R, or python.</p>
  <p>Thank you!</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2021-08-29T08:23:39.873Z
Comments.Text: When you say "consensus sequence", do you mean a genome sequence (genome assembly)? Or do you want to correct the reads? Medaka is normally used to correct existing assemblies. It looks like ARTIC is mostly amplicon-based, though I could be wrong about that. If what you want is to take fastq files and assemble a new genome sequence without a reference sequence, you probably want a genome assembler. Are your reads DNA, cDNA, direct RNA sequencing, something else? If RNA, maybe try rnaSPAdes: https://cab.spbu.ru/software/rnaspades/. If DNA, you could try raven: https://github.com/lbcb-sci/raven
Comments.UserDisplayName: Maximilian Press
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2021-09-02T04:16:51.900Z
Comments.Text: I think you are confused about the process. `Medaka` is not covid specific. Use `Medaka` if you've used it in the past or are familiar with it.
Comments.UserDisplayName: Ammar
Tags: <r><python><bioconductor><software-recommendation>
Title: How to get a consensus sequence from a nanopore fastq files?
ThreadText: # How to get a consensus sequence from a nanopore fastq files?
  
  (Asked by: username_0 on 2021-08-29)
  
  I am new in bioinformatic field. I would like to know a way to generate a consensus sequence from nanopore fastq files (fastq files demultiplexed).
  
  I usually generate a consensus sequence with "MEDAKA" of artic protocol, but it is used to generate a SARS CoV 2 sequence only.
  
  I would like to know a differente way to do it with another program, R, or python.
  
  Thank you!
  
  **Tags:** r, python, bioconductor, software-recommendation
  
  > **Comments:**
  > **username_1**: When you say "consensus sequence", do you mean a genome sequence (genome assembly)? Or do you want to correct the reads? Medaka is normally used to correct existing assemblies. It looks like ARTIC is mostly amplicon-based, though I could be wrong about that. If what you want is to take fastq files and assemble a new genome sequence without a reference sequence, you probably want a genome assembler. Are your reads DNA, cDNA, direct RNA sequencing, something else? If RNA, maybe try rnaSPAdes: https://cab.spbu.ru/software/rnaspades/. If DNA, you could try raven: https://github.com/lbcb-sci/raven  
  > **username_2**: I think you are confused about the process. `Medaka` is not covid specific. Use `Medaka` if you've used it in the past or are familiar with it.  
  
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  ## 0 answers
  
  