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Vini2 / phables

🫧🧬 From fragmented assemblies to high-quality bacteriophage genomes
https://phables.readthedocs.io/
MIT License
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Generating assembly graph #38

Closed ellasiera closed 4 months ago

ellasiera commented 5 months ago

Thank you for including recommendations for generating assembly graphs. However, since most of us don't generate that graph by default, and aren't fluent in assembly-graph-ing, it would be great to have some more detail. For example, when using Megahit, there is a tool that gets the assembly graph from contigs of a certain kmer, but not of everything. Which graph should we use in this case? Ideally you could add a feature that extracts an assembly graph in GFA given a contigs file and an assembler type, but I understand if that's beyond the scope of phables.

Vini2 commented 4 months ago

Hi @ellasiera,

Thanks for your interest in Phables!

Of course, I will add some more details on generating assembly graphs for different assemblers in the Phables documentation.

I agree, adding a feature to generate the GFA file from the contigs file will be very useful. However, most popular tools do generate a GFA file and only a few assemblers don't. So at the moment, I'm not focused on adding any new features to Phables.

Thanks!

Vini2 commented 4 months ago

Hi @ellasiera,

I've updated the Phables assembly documentation with more details on processing assembly graphs. Please feel free to re-open this issue and let me know if you have any further questions.

Thanks!