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Contig longer than mitochondrial sequence. Explanation ?

Hi,

I am trying to look for mitochondrial sequence in my genome assembly.

I have found a contig which correspond to it but the size is longer than expected (contig: 30 kbp while the mitochondrial sequence should be 16 kbp)

I am looking for explanation other than assembly error (I have pacbio data). Any ideas ?

Thanks

mitochondrial contig
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updated by vmicrobio vmicrobio • written by Picasa Picasa

Known genome? A close relative available? If yes, then assembly error is likely the only explanation. What does blast/blat'ing show?

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written by GenoMax GenoMax

If you expect a circular mitochondrial genome, it is possible that the ends of the assembled contig overlap, which makes it longer than the expected. You can check it fairly quick by aligning the contig to itself (e.g. with Gepard).

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written by alex.zaccaron alex.zaccaron

1 answer

You may have some similar patterns in your mitochondrial which will generate errors during assembly.

What de novo assembler did you used? which parameters? You may try more stringent parameters or another software

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written by vmicrobio vmicrobio

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