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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!

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  • $\begingroup$ 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: cab.spbu.ru/software/rnaspades. If DNA, you could try raven: github.com/lbcb-sci/raven $\endgroup$ Aug 29 '21 at 8:23
  • $\begingroup$ 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. $\endgroup$
    – Amar
    Sep 2 '21 at 4:16

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