mitochondrial assamply use NOVOplasty

Question

[m90]

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?

[lieven.sterck]

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)

[m90]

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

[lieven.sterck]

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

Answer 1

[cfos4698]

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