Trouble in assembling plant mitogenome

[curtainDian]

Hi, Mr. Kinggerm. I adjust my parameters from many aspects (--max-reads -w --reduce-reads-for-coverage ), but nearly all of the results are incomplete. One of the files of get_org.log.txt is below, could you please offer me some advice ? Thanks !
get_org.log.txt

[Kinggerm]

Please provide a visualized version of the *fastg file (preferred for your data privacy) or the original fastg file

[curtainDian]

okay，it’s my visulalized version of the *fastg file.

[Kinggerm]

First of all, there is no guarantee for the completeness of plant mt using Illumina data. The completeness rate is extremely low because of repeats. I always recommend only working with scaffolds.

The graph seems to be fragmented with a small number of repeats. For this dataset and a completeness goal, I would

1. not use --max-extending-len for mitogenome extension.
2. use a slightly smaller word size; and/or with less or more reads.