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3.4 years ago
SUDOsundu
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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!
Hi Sudosundu,
please include which species you are working on. Is it human? Just towards terminology,
minimapis 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 byRefseq DNA file, can you give a link?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/
It is usually helpful to mention what your final aim is, for us to put you on the right track.
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.
Then you need an
assembler, not analigner.Do a bit of googling around
canuand it's brethren to get you started. You won't need a reference sequence for this.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).
Now I am using the reference genome from the NCBI.