Jianjun Jin

File not found. Besides, with only the Illumina data, one should expect no complete mitogenome in most cases due to the abundant repeats. Even without repeats, GetOrganelle is not used...

https://github.com/Kinggerm/GetOrganelle/wiki/FAQ#why-are-there-so-many-path_sequencefasta-files

Please visualize the `*.fastg` file, not the `*.gfa` file

Please keep the upper-left component and manually remove all other components, then re-visualized the modified graph with name, depth, length, and label from *.csv marked

You should first determine whether it is organelle-sufficient graph. If you cannot determine, please attach the fastg-based graph file (can be png visualized using Bandage for data privacy) here.

For determine organelle-sufficient graph, you may also refer to https://github.com/Kinggerm/GetOrganelle/issues/122#issuecomment-1005368502

@kibzhulab Thanks for reaching out and for following the right proper thread. Please visualize the *.fastg file rather than the *.gfa file. Please provide the visualization of *.fastg file for...

Those from 100x through 300x depth contigs are more likely to be the embplant_pt contigs. You can set depth range in the Bandage, e.g. 50x ~ 500x to see the...

It can be assigned by using the command line parameter `--config-dir` for a "get_organelle_from*.py" single run, or by using the shell environment variable `GETORG_PATH` for the entire running environment. You...

Repeats in beetle mitogenomes are difficult. It's beyond the data capability of short read sequencing. AFAIK, increasing kmer helps resolving some short tangled nodes but can't get you a circular...