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cultivarium / MicrobeMod

A toolkit for exploring prokaryotic methylation and base modifications in nanopore sequencing
MIT License
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support for previously annotated genome in annotate_rm #5

Closed alexweisberg closed 6 months ago

alexweisberg commented 8 months ago

Hi, this tool looks fantastic and should be a great resource. Thanks for developing it.

I was looking at the annotate_rm tool and it seems like it could be sped up if it supported a user-supplied annotated genome (i.e. from bakta or prokka) in gbk or gff3 format as input. That way it would not need to annotate ORFs with prodigal. This would also provide the benefit of linking the RM loci to known locus tags.

This isn't necessary but it could be a useful feature. Thanks!

alexcritschristoph commented 8 months ago

Definitely, will work on this soon. Is GenBank or GFF3 preferred from your perspective?

alexweisberg commented 8 months ago

I know people differ on preferences on this but I think GenBank is typically easier as the format is more consistent, and it always includes the nucleotide sequence as well.

Alex On Nov 15, 2023 at 9:40 AM -0800, Alex Crits-Christoph @.***>, wrote:

Definitely, will work on this soon. Is GenBank or GFF3 preferred from your perspective? — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you authored the thread.Message ID: @.***>

alexcritschristoph commented 6 months ago

Included in https://github.com/cultivarium/MicrobeMod/pull/14 - let me know if there are any issues!