Do I Need To Perform Scaffolding For Reference Based Assembly Result ?
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8.9 years ago
vibhanim.21 ▴ 40

i had performed reference assembly using MIRA and had got only one single contig. now i have a doubt whether should i perform scaffolding for my data.. ?

reference assembly scaffolding • 2.5k views
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8.9 years ago

No, you can't scaffold one contig, you need at least two contigs. Also with reference based assembly, the reference sequence will guide the order of potential contigs and doesn't require scaffolding. If you wish to know if your result is valid or not we need more information from you. If the length of the single contig is about the length of the reference, that is a good sign.

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the length of my contig is 2693504 bp and that of reference is 2692570 bp . i think this is good ...

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your contig is almost 1kb longer than the reference, any idea why?

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i have no idea why... is this a bad result ?

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Google suggests your reference may be http://www.ncbi.nlm.nih.gov/nuccore/NC_016912.1 :-) If the reference is circular, maybe the end of your contig overlaps 1 kb with the beginning?

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Yes, good point, I think that is the reason, so you can scaffold it! With itself.

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thank you i will try scaffolding within itself .

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