Amplicon

As we all know, there are multiple different approaches to genome sequencing. I'll list my interpretation of the different approaches below:

• WGS - Is a rather broad term, but generally refers to single isolate sequencing. This could be for example sequencing the entire genome from a single bacterial colony.
• Shotgun - Generally refers to sequencing the entire genomes from multiple taxa (metagenomic sample). For example, sequencing a gut sample from a patient.
• Amplicon - Is a targeted approach, commonly used with PCR. The goal here is to sequence a part of the target genome. One example is amplicon sequencing of the 16S bacterial rRNA region.

Amplicon sequencing has several advantages compared to other sequencing protocols:

• Reduced costs per sample due to sequencing less DNA for a shorter period of time.
• Enables sequencing more samples in parallel due to smalles sample sizes.
• The bioinformatic analysis is generally less computationally heavy.

However, this does not come without disadvantages:

• PCR can introduce artifacts.
• Off targets, depending on the primer design.
• Reduced genomic resolution.

In the following chapters, we'll go through some very basic Rust implementations of common amplicon based analyses.