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Newbler vs minia

| posted 08 Apr, 2020 17:55
Dear all,

As Newbler is deprecated, we assembled "our" phage genome in class using "minia" – a short-read assembler based on a de Bruijn graph. Our assembly looks similar to the one created using Newbler but is slightly shorter (141kb vs 151kb) - any idea why this might be the case?
How can we find out what type of ends our genome has?

Thank you in advance for your help!

| posted 09 Apr, 2020 00:23
Hi Susanne,

The length disparity is almost certainly because of the terminal repeat. When I assembled your genome, it looked clear to me that your it had direct terminal repeats; there was an area of approximately double coverage (compared to the rest of the genome) and flanking reads that started on the same base. That's classic terminal repeat.

In those cases, we generally report the genome with the terminal repeat on each end, as the DNA would actually appear in the phage capsid. The Metroid terminal repeat is around 10kb, which almost certainly accounts for the difference between your assembly and the final file. My initial assembly was also only ~140 kb, but once I added the second copy of the repeat, it went to ~150kb.

Hope that makes sense,
| posted 09 Apr, 2020 15:43
It does, thanks Dan!
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