Amplicon sequencing reads a defined PCR product deeply rather than a whole genome broadly, which makes it the cheapest way to answer a targeted question: which bacteria are in a sample, which variants a set of loci carry, how efficiently a CRISPR edit landed. Services sell it per sample with library preparation, sequencing and often a first-pass analysis bundled. This page explains the applications, what to require of a service and how the per-sample price is built, then points at the vendor comparison.
The applications that use it
Microbial community profiling amplifies a marker gene such as the bacterial 16S ribosomal RNA gene or the fungal internal transcribed spacer and classifies the reads. Targeted variant detection amplifies a panel of loci to call mutations at depth. Editing analysis amplifies the edited locus to measure the fraction of reads carrying each outcome. The primers differ, the analysis differs, and services usually price these as separate products even though the sequencing is the same.
What a service should deliver
Ask what is included per sample: DNA extraction or not, the primer set and its region, library preparation with sample indexing, the sequencing platform and read length, a minimum read count per sample, and the analysis deliverable. Demultiplexed reads should always be provided; a taxonomic table, a variant table or an editing-outcome report is the analysis layer and should be named explicitly. Controls matter too, so ask whether a mock community or a no-template control is run and reported.
How the price per sample is built
The per-sample price falls as the batch grows because the sequencing run is shared, so a quote for a handful of samples and a quote for a full plate are different numbers. Extraction, custom primers, deeper reads and analysis each add a line. Turnaround is usually quoted from receipt of samples that pass quality control, which is worth reading carefully when a project has a deadline. The comparison on this site records each vendor's published sequencing service prices, verified on the vendor's page and dated.
Amplicon or shotgun
Amplicon sequencing gives taxonomy at genus level cheaply and at scale but says nothing about function and inherits any bias of the primers. Shotgun metagenomic sequencing reads everything and resolves species and genes, at a higher price per sample and a heavier analysis. For a targeted variant question, amplicon sequencing is nearly always the right tool; for an open question about what a community does, it is the survey before the deeper study.
Questions people ask about amplicon sequencing
What is amplicon sequencing used for?
Microbiome profiling with marker genes, targeted mutation detection across a panel of loci, and measuring CRISPR editing outcomes at a locus.
What do I send to an amplicon sequencing service?
Extracted DNA or, at some services, the raw sample; the primer set or the target region; and the read depth and analysis you want. Each service publishes its sample requirements.
How deep should amplicon sequencing be?
Deep enough to see the rarest member or variant you care about with confidence; services quote a minimum read count per sample and deeper tiers cost more.
Is 16S sequencing the same as amplicon sequencing?
16S sequencing is one application of amplicon sequencing, targeting the bacterial ribosomal RNA gene; the same method serves fungal, variant and editing readouts.