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PacBio Amplicon Analysis (pbaa) separates complex mixtures of amplicon targets from genomic samples. The pbaa application is designed to cluster and generate high-quality consensus sequences from HiFi reads.
PacBio Amplicon Analysis (pbaa) is designed to cluster and generate high-quality consensus sequences from HiFi reads. The tool can separate complex mixtures of amplicon targets like HLA and genes with pseudogenes or paralogs.
Here, we present an amplicon sequencing workflow for characterization of full-length CYP2D6 alleles from samples of 100 ng of human genomic DNA (gDNA). In the first-round PCR, LA Taq DNA polymerase (Takara: RR02AG) and two primer pairs listed in Table 1 are used to generate 9 kb and 12 kb PCR products.
Amplification can generate off target reads. Similarly, pbaa can accidentally place a few reads in the wrong grouping/locus. These reads may generate clusters that are off-target (not amplified). By providing a list of guide-names / group-names (one per line), pbaa
Amplicon Analysis with Guided Clustering (pbaa) requires a file of reference sequences in FASTA format to use as a the cluster guide. The program can accept any valid FASTA-format sequence file, but using a well curated sequence file for the cluster guide will provide for faster, higher quality results. This document offers some pointers on how ...
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PB Amplicon Analysis (pbAA) Generates phased consensus sequences by clustering HiFi reads. The output of pbAA is ideal for diplotyping complex loci of biomedical interest such as HLA genes or CYP2D6.
