Is assembly graph organelle sufficient?

[karthickbrlab]

after running getorganelle, i visualized using bandage.

Kindly check the attached graph. Does this an complete assembly. WHETHER IT IS ORGANELLE SUFFICIENT

extended_K105.assembly_graph.fastg.extend-embplant_pt-embplant_mt.fastg

Secondly, there were single Inverted repeat sequence in the genome. Does the assembly merged two inverted repeat into one?

[JianjunJin]

1. It is organelle sufficient. You should obtain two fasta files out from get_organelle_from_reads.py (see here for why there are two).
2. This is a graph representation of the assembly, where two inverted repeats are identical and surely represented as one. However, the two repeats will be preserved in the linearized form - fasta files, see the same link above and also see the examples to learn more.

[karthickbrlab]

I just used getorganelle from assembly graph to extract the circular cp genome from the fastg/gfa files.. I did visualized using ogdraw.. I think I have got it right. Thanks for your assistance. Karthick

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On Wed, 3 Apr, 2024, 2:36 am JianJun Jin, ***@***.***> wrote: 1. It is organelle sufficient. You should obtain two fasta files out from get_organelle_from_reads.py (see here <https://github.com/Kinggerm/GetOrganelle/wiki/FAQ#what-are-the-differences-of-complete1path_sequencefasta-and-complete2path_sequencefasta-output-files> for why there are two). 2. This is a graph representation of the assembly, where two inverted repeats are identical and surely represented as one. However, the two repeats will be preserved in the linearized form - fasta files, see the same link above and also see the examples to learn more. — Reply to this email directly, view it on GitHub <#321 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/BBQ4H44AKWII4WXOKPLBEUDY3MMUTAVCNFSM6AAAAABFKPTB36VHI2DSMVQWIX3LMV43SRDJONRXK43TNFXW4Q3PNVWWK3TUHM4DSOBZGQ3DE> . You are receiving this because you authored the thread.Message ID: ***@***.***>