Reference sequence to be used for assembly in nanopore
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2.7 years ago
SUDOsundu ▴ 60

Hello,

I am a newbie in NGS data analysis. I wanted to analyse the Oxford nanopore's reads. For assembly I am using minimap tool. A reference file is needed for the process. Can I use any related/similar fasta sequence as a reference file or I must use only the Refseq DNA file? Need some help!

reference Assembly • 838 views
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Hi Sudosundu,

please include which species you are working on. Is it human? Just towards terminology, minimap is an aligner so it matches DNA sequences to a reference. Assembly would be to put the raw reads together (=assemble) a new reference/contig/genome/whatever-you-sequenced. What do you mean by Refseq DNA file, can you give a link?

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Hi Sorry for the less information. I am working on plant virus. My aim is to characterize the viral genome. Refseq DNA file means reference genome to be used for mapping the reads. https://www.ncbi.nlm.nih.gov/refseq/

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I wanted to analyse the Oxford nanopore's reads.

It is usually helpful to mention what your final aim is, for us to put you on the right track.

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Hi, I just came through your Nanopack. Thanks for the pack. My final aim is to characterise the plant viral genome. I am sequenced virus infected plant samples and to characterize them based on a reference viral genome.

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Then you need an assembler, not an aligner.

Do a bit of googling around canu and it's brethren to get you started. You won't need a reference sequence for this.

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Can I use any related/similar fasta sequence as a reference file or I must use only the Refseq DNA file?

You could use a related reference but you will need to keep in mind that depending on how different that strain/species is from your organism the results may be less than optimal. That said, if a RefSeq genome is available then that is your best bet for use as a reference for alignment (though it could also be used for a reference guided assembly).

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Now I am using the reference genome from the NCBI.