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Battling PCR bias in 16S microbial sequencing
Second and third-generation sequencing is letting labs dig deep into microbial communities for genomic information. 16s rRNA metagenomics sequencing is an approach used in biomedical labs, in hospitals and in field research to quickly identify bacteria in a given sample. It is especially useful for identifying bacteria that are hard or impossible to cultivate in the lab. The use of rRNA sequence helps to study and realign phylogenetic trees. Scientists can go deep into sequences and identify rare variants using this technique. Microbial surveys using 16S rRNA sequencing are fast, cheap and popular, but they are also plagued by PCR bias. When GC levels are high, hairpins develop and they might interrupt PCR-based amplification or make amplification impossible. Some microbes remain undiscovered and the quantities of different strains are misjudged. There are various strategies used to battle bias in metagenomics sequencing projects.
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