amplicons

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AMPtk: Amplicon ToolKit for NGS data (formally UFITS)

Design degenerated primers on highly variable alignments for full genome sequencing or qPCR. Specifically developed for viruses.

Classify output of AmpliconArchitect to detect types of focal amplifications present

Some NGS library preps use amplicons, and it can be difficult to determine the coverage and depth of each amplicon.

pyAmpli: an amplicon-based variant filter pipeline for targeted enriched resequencing data

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