Guidelines for Genexus
™
Integrated Sequencer operation
• Follow guidance that is provided by Genexus
™
Software when you create a run
plan to determine which consumables must be loaded and which consumables
can be reused from a previous run.
• Follow guidance that is provided by the software when you create a run plan to
determine how many samples can be run with a given assay or assays in an
instrument run. The number of samples that can be included in a sequencing run
depends on multiple factors.
Limiting factor
Description
The number of
available barcodes in
the barcode plate
The maximum number of available barcodes per run is 32.
IMPORTANT!
When libraries are prepared on the
Genexus
™
Integrated Sequencer, each target amplification
reaction for a sample requires a unique barcode.
Maximum number of
target amplification
reactions per run
One library strip pair has the reagents necessary for 4
target amplification reactions, or 4 barcodes. With a
maximum of 8 library strip pairs loaded, a maximum of
32 samples can be run using an assay with one primer pool.
The number of primer
pools per assay
Given the limits of 32 target amplification reactions, and
32 available barcodes, the number of samples in a run
multiplied by the total number of primer pools in the assays
that are used in a run cannot exceed 32.
For one single
‑
pool assay, a maximum of 32 samples can be
run on a single chip. If you are using 2 assays with two
primer pools each, you can sequence a maximum of 8
samples in a run. Similarly, for one assay with 4 primer
pools, you can sequence a maximum of 8 samples in a run,
if the minimum read count per sample allows it.
The number of unused
lanes on an installed
chip
A maximum of 4 lanes are available on a single GX5
™
Chip.
The minimum read
count per sample for
an assay
The minimum read count per sample parameter is set
during assay creation.
• Two assays cannot share a chip lane, so a maximum of 4 assays can be run per
chip.
• The assays that are used in a single run must use the same chemistry (Ion
AmpliSeq
™
or Ion AmpliSeq
™
HD), and have compatible cycling parameters to
allow amplification in the instrument thermal cycler. The thermal cycler has two
independently controlled heating zones. After you select an assay, Genexus
™
Software restricts the list of available assays to use in the run to those that are
compatible with the selected assay or assays.
• One library strip pair is required for each primer tube position 1–8 that is filled in
a run.
• One template strip pair is required for every chip lane that is used in a run.
• Consumables are configured to support sample batch sizes in multiples of four
samples. The most efficient use of consumables occurs when samples are run in
multiples of four.
Chapter 2
Before you begin
Guidelines for Genexus
™
Integrated Sequencer operation
2
24
Genexus
™
Integrated Sequencer User Guide
