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bxlab / metaWRAP

MetaWRAP - a flexible pipeline for genome-resolved metagenomic data analysis
MIT License
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Quant_bin as read recruitment method/alternative #285

Open blancaverag opened 4 years ago

blancaverag commented 4 years ago

Dear developer,

Thank you for your pipeline!

I have a question regarding quant_bins module. I first thought of this module as an improved method for metagenomic read recruitment, able to compute coverage of bins/genomes in whichever metagenome, not just in the ones they were extracted from. But this is not the case because quant_bins module needs contigs in bins and assembly files to have the same names. Hopefully, you could help me understand the rationale behind this module not allowing different names on contigs, and, therefore, not constituting an alternative method for metagenomic read recruitment.

ursky commented 4 years ago

I don't really see the issue here - this is a practical limitation of the method, not the software. The abundance estimation for a MAG will be more accurate in the context of the whole assembly, but the module absolutely does support abundance estimation without providing the assembly (its just not recommend it if you can avoid it).