amplicons

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

AMPtk: Amplicon ToolKit for NGS data (formally UFITS)

next-generation-sequencing amplicons microbiome mycobiome fungi rdna coi lsu co1 mtco1

Classify output of AmpliconArchitect to detect types of focal amplifications present

python-library amplicons focal double-minutes bfb ecdna ampliconarchitect

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

coverage bioinformatics python3 depth amplicons samtools

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

bioinformatics genomics mips somatic-variants ngs variants amplicons germline ngstools variant-filtration targeted-sequencing haloplex

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