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mitochondrial assamply use NOVOplasty

Hello there,

I have assembled the mitochondrial genome for the species "Gazelle using NOVO plasty ." I have a reference sequence for this species, as well as the cytb gene sequence. However, I've noticed something unusual: the reference and query assambly sequence do not start and end at the same positions. Can someone explain why this might be the case? enter image description here

mitochondrial genome mammles
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updated by dr_cfoster dr_cfoster • written by m90 • m90

most (all?) mitochondrial genomes are circular so you can actually 'cut' them to a linear representation anywhere you want.

(by which I mean that it's actually simply arbitrary where the linear version starts/stops)

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written by lieven.sterck lieven.sterck

So this means , the direction it takes not mean the assambly was wrong , right? Because i made assambly assessment and it gives me high quality score

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written by m90 • m90

no indeed, the assembly itself will be just fine, it just decided to 'break' the circle on a different location.

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written by lieven.sterck lieven.sterck

1 answer

You might want to consider trying to rotate the circular genomes to a common start position. A new-ish tool is available for this purpose: "Rotate: A command-line program to rotate circular DNA sequences to start at a given position or string " https://wellcomeopenresearch.org/articles/8-401

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written by dr_cfoster dr_cfoster

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