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The 16S-SNAPP pipeline attempts to generate consensus sequences from reads mapped to the same reference sequences.
Depending on differential primer efficiency, the completeness of the reference set, the sequencing depth and read length, the 16S-SNAPP pipeline is able to generate consensus sequences of various lengths and approaching near full-length sequences of specific variable regions.
However, the panel lacks phasing and amplicon sequences cannot be linked together due to the complex composition of a metagenomic sample.