Getting multiple "Disentangling Failed" even after changing settings.

[giorge-costa]

Dear Dr. Jin

I am very new to the bioinformatics field, and have recently started using GetOrganelle for my research project. I have been trying to assemble an animal mitochondrial genome, but am currently facing the "Disentangling Failed" problem, even after trying to change the settings as appointed in the FAQ. Could you please give me a hint to what I'm doing wrong?

I have run GetOrganelle three times, and got these outputs:

First try:

1_get_org.log.txt

Second try:

2_get_org.log.txt

Third try:

get_org.log.txt

Thank you so much in advance.

Best regards, Giorge

[JianjunJin]

According to the graph, the second and third tries generated organelle-complete graph, which is improved from the first try.

However, there are too many repeats within this graph, making it unsolvable with short-read data. So, there is no way to get a complete mitogenome from current data, while the contigs are still usable for phylogenetic analysis.

[zhengyanstu]

I have met a similar problem and generated a more complicated graph. Too many short reads made it hard to separate different mitochondrial DNA loops. Could you give me suggestions to solve this problem?

[Kinggerm]

I have met a similar problem and generated a more complicated graph. Too many short reads made it hard to separate different mitochondrial DNA loops. Could you give me suggestions to solve this problem?

As I mentioned, there is no way to get a complete mitogenome from short reads. You may use long reads or the current incomplete result, depending on your research purpose.

[zhengyanstu]

Thanks a million