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Amplicon vs shotgun (whole genome) sequencing
Metagenomic shotgun sequencing[edit]
Having reads of 400-500 base pairs length is sufficient to determine the species or strain of the organism where the DNA comes from, provided its genome is already known, by using for example a k-mer based taxonomic classifier software. With millions of reads from next generation sequencing of an environmental sample, it is possible to get a complete overview of any complex microbiome with thousands of species, like the gut flora. Advantages over 16S rRNA amplicon sequencing are: not being limited to bacteria; strain-level classification where amplicon sequencing only gets the genus; and the possibility to extract whole genes and specify their function as part of the metagenome.[19] The sensitivity of metagenomic sequencing makes it an attractive choice for clinical use.[20] It however emphasizes the problem of contamination of the sample or the sequencing pipeline.[21]
Full length amplicon vs hypervariable regions
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https://nf-co.re/ampliseq/2.9.0/docs/usage#taxonomic-classification
ASV vs OTU
Illumina vs Nanopore sequencing technologies
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Amplicon analysis workflow
Reference paper
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