Jianjun Jin

That's cool. I've conducted some simple tests on organelle genome assembly using flye/canu based on ONT/SMRT reads. The result is not promising even after polish, e.g. the IRs in chloroplast...

GetOrganelle mainly benefits from two aspects of the data: 1. The target has higher sequencing depth than the background non-target (when de novo assembling the target from reads), so that...

Currently GetOrganelle does not support long read extension. But you may also refer to this related [issue](https://github.com/Kinggerm/GetOrganelle/issues/73)

Hi Edgardo, Thanks for using GetOrganelle and for the kind suggestion. I will carefully consider and test it. As for Ericaceae, it will still be difficult with only illumina data....

> Hi，I conducted GetOrganelle and found these Errors like this: > > GetOrganelle v1.7.1 > > get_organelle_from_reads.py assembles organelle genomes from genome skimming data. > Find updates in https://github.com/Kinggerm/GetOrganelle and...

@harish0201 That's true. But currently pigz is not required for non-conda installation. Further incorporating needs more testing in different environment, it's on my plan though. Thanks for the suggestions.

Unfortunately, there is barely hope for achieving a complete mitogenome with current Illumina data. According to the graph, there are many cp->mt transfers and many repeats that Illumina data cannot...

1. Clean the graph to achieve a pt+mt complete graph with both pt and mt contigs. Remove the up-left short-repeat contigs, I believe those are not organelle contigs. 2. Map...

> can you describe in detail the following operation? > > > 1. Clean the graph to achieve a pt+mt complete graph with both pt and mt contigs. Remove the...

Please try '--reduce-reads-for-coverage inf --max-reads inf' first, it could be caused by wrong estimation of the target depth.