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bcgsc / NanoSim

Nanopore sequence read simulator
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Coverage breadth following metagenome characterization #205

Closed ezherman closed 2 months ago

ezherman commented 2 months ago

Hi, thanks for building this awesome tool! I have been playing with the metagenome abundance profile feature of NanoSim. I am interested in estimating coverage breadth (and depth) following quantification with read_analysis.py metagenome and the options -gl -c -q --no_model_fit.

Is it possible to infer the reference position to which each base was assigned from the NanoSim output?

kmnip commented 2 months ago

If I am not mistaken, metagenome abundance is quantified based on fractional assignment of reads using an EM algorithm. So, no additional information is inferred on individual base of each read used during quantification.

ezherman commented 2 months ago

Hi @kmnip, thanks for getting back to me. Yes, makes sense now that I've looked at the EM algorithm more closely. I can imagine an extension may update the read assignment given perc_for_species for reads in multi_mapped_reads, but I'm not in a position now to play around with that!