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Analysis of the microbiome: Advantages of whole genome shotgun versus 16S amplicon sequencing
Our study demonstrates that whole genome shotgun sequencing has multiple advantages compared with the 16S amplicon method including enhanced detection of bacterial species, increased detection of diversity and increased prediction of genes. In addition, increased length, either due to longer reads or the assembly of contigs, improved the accuracy of species detection.
Full length amplicon vs hypervariable regions
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The 16S rRNA gene is about 1,500 bases in length. Illumina reads are much shorter than this, therefore amplicon analysis typically involves sequencing 2-3 ‘hypervariable’ 16S regions.
https://www.nature.com/articles/s41598-023-30764-z
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Different groups of bacteria are better represented by specific regions.
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