<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>

CC BY-SA 4.0
2021-08-29T08:23:39.873Z
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
Maximilian Press
CC BY-SA 4.0
2021-09-02T04:16:51.900Z
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.
Ammar
<r><python><bioconductor><software-recommendation>
How to get a consensus sequence from a nanopore fastq files?
# 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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