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What is metagenomics?
Amplicon vs shotgun (whole genome) sequencing
Full length amplicon vs
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hypervariable regions
16s/18s/ITS, etc
Workflows
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Functionally, the longer 3rd gen reads can counter the higher error rates through increased number of potential base matches. For 16S rRNA sequencing, short read Illumina sequences typically cover two 16S hypervariable regions, whereas Nanopore sequences the full 1.5 kilobase 16S sequences, which includes all nine hypervariable regions.
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This 2023 paper compared Illumina and Nanopore shotgun sequencing for identifying bacteria strains with little genomic variation between them. Both Illumina and Nanopore were able to correctly identify the bacteria strains, despite the higher error rate of the Nanopore sequences.
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