Too many results due to palindromic repeats about getorganelle HOT 6 CLOSED

Hi @Li-Rui091

This is an interesting and exciting result! Thanks for the log file and Bandage image, very helpful.
Please check whether the lengths of those small dotted contigs (which are actually small palindromic repeats) are always equal or smaller than 170 bp. If all of them are no larger than 170 bp, those 512 paths could be reduced to 2 paths, meaning each set of 256 paths are actually the same.
Please let me know the updates! I will add module for handling those palindromic repeats automatically in the coming version, which would then automatically reduce 512 to 2 if applicable. Your feedback will be of great help to this.

Best,
J

from getorganelle.

Hi, @Kinggerm,
I checked the lengths of those small dotted contigs,they are between 94bp and 170bp.

from getorganelle.

Hi @Li-Rui091
Please randomly pick some, like 10 of those 512 sequences and conduct a whole sequence alignment. I think there will be only two kinds of seqs in total. Please help me confirm my guess.
Thanks!

from getorganelle.

Hi, @Kinggerm,
I randomly pick 10 of those 512 sequences and conduct a whole sequence alignment,The alignment results show that all sequences are completely identical.However, I annotated the ten sequences separately, but produced two results, one of which annotated nine genes more than the other.

from getorganelle.

If sequences are completely identical, it should be the problem of the annotation tool.
Also, please be aware that there should be two kinds of seqs in total, mainly differing in SSC direction, which are both correct.

I think your assembly issue is solved and I close this issue. Feel free to open it if you have more questions on assembly.

from getorganelle.

I have updated GetOrganelle to 1.6.3, which will recognize the palindromic repeats and suppress a large amount of redundant repeated paths.
You're invited to have a try! If you would like to try, please report any interesting results here. Your feedback will be very helpful to GetOrganelle. Thanks in advance!

from getorganelle.