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AmpliconSuite / AmpliconSuite-pipeline

A quickstart tool for AmpliconArchitect. Performs all preliminary steps (alignment, CNV calling, seed interval detection) required prior to running AmpliconArchitect. Previously called PrepareAA.
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Guidance on creating reference genome files for a new species #61

Open YxZhang-XHCY opened 1 week ago

YxZhang-XHCY commented 1 week ago

Dear AmpliconSuite Developers,

First of all, thank you for developing such a great software that provides a lot of convenience for ecDNA research. I encountered a little difficulty when trying to apply AmpliconSuite to the rice (Oryza sativa L.) genome. The species currently supported by AmpliconSuite are relatively limited, and our lab mainly studies plant genomes, especially rice.

I wonder if you could provide some guidance on how to create reference genome files for a new species so that AmpliconSuite can analyze ecDNA in that species? I have the following main questions:

In addition to the FASTA sequence of the genome, what other annotation files need to be prepared? What are the format requirements for these annotation files? Are there any recommended generation tools or pipelines? How should AmpliconSuite's configuration file be modified to add a new species? Your guidance would greatly benefit our research on plant ecDNA.

Thank you very much!

Best regards,

Yaoxin

jluebeck commented 1 week ago

Hi, I have just added a FAQ entry to our Guide document answering this question here. It is very difficult to assemble annotations to construct an AA data repo and it requires lots of work and testing even if the annotations are available.

I want to also reiterate that AmpliconArchitect is for studying focal amplifications in cancer genomes. For small circular extra-chromosomal DNA (eccDNA), on the order of 100-1000bp, you should not use AmpliconArchitect at all.

Thanks, Jens

YxZhang-XHCY commented 1 week ago

Thank you very much for your prompt and detailed response, as well as for adding the relevant FAQ entry to the guide document. We understand the complexity and the significant amount of work and testing required to construct an AA data repository. Your guidance is extremely helpful to us.

Best regards, Yaoxin