Custom/PCR Amplicon

The Custom/PCR Amplicon workflow evaluates short regions of amplified DNA (amplicons) for variants. The focused sequencing of amplicons enables high-coverage sequencing of particular regions across many samples. The main output files generated by the Custom/PCR Amplicon workflow are BAM files (containing the aligned reads) and VCF files (containing the variant calls).

The Custom/PCR Amplicon workflow supports multiple manifests (containing the probe regions) and consensus sequence reporting for multi-manifest runs.

The Custom/PCR Amplicon workflow can only be used to analyze MiSeq sequencing results

The Custom/PCR Amplicon App Results Page provides a four graphs:

The PCR amplicon Sample Details page provides six panes:

The graphs and variants table display data for the amplicon that is selected in the Amplicon Table.


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