When analyzing targeted microbiome sequencing, a different approach to determining the origin of the sequence is required than typical alignment-based methods. This is because the gene of origin for an amplified target gene is already known, and the goal is to determine its taxonomic origin based on a small number of variations relative to similar taxa.
In the context of whole-genome sequencing, a small number of single nucleotide variants (SNVs) caused by sequencer error are unlikely to seriously confound an aligner and will have little effect on the final attribution of the sequence. Targeted sequencing, with comparison of multiple similar sequences rather than alignment across multiple genomes, has the potential to be confounded by erroneous SNVs.
This white paper from Zymo Research reviews the relative advantages and disadvantages of two strategies for minimizing the effects of targeted sequencing error in microbiome informatics, which has the potential to be confounded by erroneous SNVs, resulting in the detection of an incorrect organism or the false discovery of a new organism.
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