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Hi there,
If one sequences a metagenomics sample at the same depth (i.e. with same amount of data/yield) with nanopore and Illumina sequencing, can one assume that the Illumina experiment samples the environment more/better than the long-read sequencing experiment, e.g. due to the larger number of short reads compared to the lower number of long reads?
Intuition says that more reads should mean more sampling, but at the same time I think this assumes that the short reads are more likely to originate from DNA fragments that belong to different genomes, compared to the long reads. But given the details of both methods, is this a good assumption?
Thanks for your thoughts
If one sequences a metagenomics sample at the same depth (i.e. with same amount of data/yield) with nanopore and Illumina sequencing, can one assume that the Illumina experiment samples the environment more/better than the long-read sequencing experiment, e.g. due to the larger number of short reads compared to the lower number of long reads?
Intuition says that more reads should mean more sampling, but at the same time I think this assumes that the short reads are more likely to originate from DNA fragments that belong to different genomes, compared to the long reads. But given the details of both methods, is this a good assumption?
Thanks for your thoughts