Questions & Answers

Collapse All


Expand All


The adapters used in this assay are optimized for the AmpliSeq workflow. Nextera or TruSeq Adapters are not compatible with this assay.

It is possible to run 3 different AmpliSeq for Illumina designs each with barcodes on the same sequencing run. However, your target amplicon size and required coverage must be achieved in a single run.


A 2×151 bp paired-end read is recommended.  

You can manipulate coverage by increasing sequencing throughput (eg, a larger flow cell output or sequencing platform) or reducing the number of samples pooled per run.


Local Run Manager and BaseSpace Sequence Hub have apps available for analysis. The DNA Amplicon Analysis App and RNA Amplicon Analysis App are available on BaseSpace Sequence Hub. Further analysis can be performed on any variant calls using BaseSpace Variant Interpreter.  Local Run Manager has a similar DNA Amplicon Analysis Module and RNA Amplicon Analysis Module which utilizes the same workflow and algorithm as the BaseSpace Sequence Hub Apps. 

The DNA Amplicon analysis workflow can be used to perform alignment and variant calling and the RNA Amplicon analysis workflow for fusion calling.  Additionally, OncoCNV caller, a BaseSpace Lab Apps is available for CNV analysis.

For an example data from an experiment, go the Public Data page in BaseSpace.

Use BaseSpace DNA Amplicon 2.0 or higher and Local Run Manager DNA Amplicon Analysis Module v1.1 or higher can be used to analyze Sample ID.

Sample ID manifest information is built into Use BaseSpace DNA Amplicon 2.0 and Local Run Manager DNA Amplicon Analysis Module v1.1.  User only needs to click the sample ID option for analysis.  Additionally, the sample ID manifest file is available in the AmpliSeq for Illumina Panel Downloads section in the support website.

On-target bases shows the percentage of total sequenced bases that map to target regions in the reference genome. This metric reflects the percentage of bases from amplicons that a) were designed, synthesized, and pooled and b) generated sequence data mapping to the target regions.