Pooled NGS Quotes: Index Skus Failed Pools and Top-up
The effect of multiplexing on NGS cost per sample is a change in the billed unit, not a cheaper instrument. Adding barcodes spreads one lane across more libraries and shrinks each sample’s unique reads. Prefer a pooled quote only when the index SKU, the minimum unique-read target, and the failed-pool rule are written as separate lines. Reject a per-sample card that is silent on those three. The 2026 NGS cost overview still owns recipe, depth, and library-prep scope. Sanger versus NGS cost still owns method-versus-method money. This page only explains how pooling edits the per-sample number. Zettalab does not sell sequencing and has no official NGS price. Public pricing-card conflicts on the software site are recorded elsewhere and are not synthesized here.
Per-Sample Cards Hide the Index and the Failed-Pool Lines
The search is how multiplexing changes ngs cost per sample. Illumina’s multiplexing note states the operational fact: barcodes let many libraries share one run. That sentence is why a per-sample card can fall when the pool grows. It is also why depth can fall with it. A 2018 index-swap study adds a second billable object: unique dual indexes cost more than a single index and exist because some flow-cell chemistries misassign reads. Those two sources do not publish a Zetta rate. They publish units. Unique dual indexes, pool QC, and a stated minimum unique-read target belong on the quote beside the kit names. After those units are named, a construct map in ZettaGene can keep the sample sheet attached to the expected alleles. The workspace does not replace a sequencer.
Three Units a Pooled Card Must Show
Three units decide whether a lower per-sample number is a real saving. They are not a vendor rank.
| Unit | What the lab is buying | How pooling moves it | Fail signal |
|---|---|---|---|
| Index SKU | Single index, combinatorial dual, or unique dual indexes | UDI kits raise the library line; they reduce misassignment risk on some platforms | The card says “indexed” and never names the index class |
| Lane share / unique reads | That library’s slice of a flow cell after barcodes are applied | More barcodes lower chemistry per sample and can starve the unique-read target | Pool size is missing, or depth is promised without a unique-read meter |
| Failed pool / top-up | Who pays when one barcode is under-represented or a library fails QC | A cheap pool becomes expensive when the weak sample is re-run | The quote is silent on repeats and top-up |
Weight the index SKU first when the instrument class is known to swap indexes. Weight lane share first when the analysis plan has a hard unique-read floor. Weight the failed-pool line first when the cohort is small enough that one dropout wrecks the study. Do not weight a cheaper-looking average copied from another lab. That average hid a different pool.
Three Pooling Postures, Same Units
The options are postures on one invoice, not a 2026 ranking of cores. Score all three on the same units.
| Dimension | Small balanced pool | Large filled lane | Urgent singleton on a high-output kit |
|---|---|---|---|
| Index SKU | Usually UDI; the kit line is visible | UDI still required if the chemistry swaps indexes | Index cost can exceed the sample’s share of chemistry |
| Lane share / unique reads | Each library can still hit the target | Chemistry per sample falls; unique reads may miss | The sample buys unused capacity |
| Failed pool / top-up | One fail is expensive but easy to see | Under-represented barcodes trigger top-up or dropouts | There is no pool to hide in; the fail is a full re-run |
| When it fits | A defined cohort with a written unique-read floor | Only if the analysis still passes after expected waste | When calendar beats fill; not because the card looks low |
Prefer a small balanced pool when every sample must hit the same unique-read floor. Prefer a large filled lane only after someone translates pool size into unique reads and names the top-up owner. Prefer an urgent singleton only when the calendar is the constraint. A half-empty high-output run is not inexpensive data. Capture-bait versus sequencer lines are a different invoice split and live on the sibling page in this batch.
Keep the Sample Sheet With the Paid Reads
Write the index class, the unique-read target, and the failed-pool owner before you store a per-sample number in a budget. ZettaGene can hold the construct and expected alleles next to that sample sheet. ZettaNote can hold the run note. Neither product sells a lane, and neither has an official sequencing rate. If those three units are still missing, the lower card is not a multiplex saving. It is an unfinished quote.
Frequently Asked Questions
Does a lower per-sample NGS card mean the pool is cheaper?
No. A larger pool can lower chemistry per sample and miss the unique-read target. Compare index class, unique reads, and the top-up rule.
Is a unique dual index included in the per-sample number?
Only if the quote names that SKU. “Indexed” is not a unique dual index. Ask which index class is inside the library line.
Related Articles