Increase the insert size length to improve assembly completeness

[zhengyanstu]

First check

• I used the GitHub search to find a similar issue or discussion and didn't find it.
• I searched GetOrganelle.wiki context, especially the FAQ and browsed the examples to confirm it is unexpected to happen.
• I have updated GetOrganelle to the latest released version

Please ask questions in the Question in GitHub Discussions unless it is a feature request or bug report.

Dear Dr Jin,
Can GetOrganelle handle data from libraries with 500bp insert size and paired-end sequencing with read lengths of 250bp each? I wonder if increasing the length of the insert sequence be beneficial for solving complex structural issues caused by repetitive sequences?

[JianjunJin]

Good question! In short, not that much with the current implementation.
But you may probably find better scaffolding results in the SPAdes outcome inside the GetOrganelle output folder, which is not fully used by current GetOrganelle versions.