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PacBio Amplicon Analysis
+*** 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. This application only works on HiFi amplicon data. There are several assumptions made within the code that will only support high quality reads (>QV20). This application will not work on CLR data. _pbaa_ is reference aided method (pseudo de-novo). -Typical use cases involve multi-allelic samples where the sample-specific ploidy or copy number is unknown. _pbaa_ can effectively separate alleles with one to many variants, including SNVs and large indels contained within the target region. _pbaa_ has been optimized and tested for datasets with a moderate (<10) cluster count. Feedback for higher cluster density is welcome and may be addressed in future releases. +Typical use cases involve multi-allelic samples where the sample-specific ploidy or copy number is unknown. _pbaa_ can effectively separate alleles with one to many variants, including SNVs and large indels contained within the target region. _pbaa_ has been optimized and tested for datasets with a moderate (<10) cluster count. Feedback for higher cluster density is welcome and may be addressed in future releases. ## Workflow  @@ -105,7 +110,7 @@ _pbaa_ supports batching of samples via the FOFN (file of file name[s]) format. Guide/reference sequence choice affects read grouping/placement. It is important to choose guides that are sufficiently divergent. If too many similar alleles are used for the same locus the fraction of un-placed reads will increase because the number of informative kmers decrease within a locus. Too few guides can also cause cluster dropout; it's the goldilocks problem. -Guide sequences should be grouped into locus assignments. For example if multiple HLA-A alleles are used in the guide sequence, they should be grouped, so clustering will be performed at the locus level. +Guide sequences should be grouped into locus assignments. For example if multiple HLA-A alleles are used in the guide sequence, they should be grouped, so clustering will be performed at the locus level. ``` Allele_1|HLA-A (sequence name | group name) @@ -177,7 +182,7 @@ m54043_190914_194303/4195156/ccs HLA-B + HLA00158_B_14-02-01-01_4070_bp|HLA-B 0. ## Best practices -### Sample preparation and sequencing +### Sample preparation and sequencing [Targeted Sequencing For Amplicons Document](https://www.pacb.com/wp-content/uploads/Application-Brief-Targeted-sequencing-Best-Practices.pdf) diff --git a/img/pbaa_card.png b/img/pbaa_card.png new file mode 100644 index 0000000..a37898c Binary files /dev/null and b/img/pbaa_card.png differ diff --git a/img/pbaa_logo.png b/img/pbaa_logo.png new file mode 100644 index 0000000..21bc3ff Binary files /dev/null and b/img/pbaa_logo.png differ diff --git a/img/pbaa_logo_transparent.png b/img/pbaa_logo_transparent.png new file mode 100644 index 0000000..a90a143 Binary files /dev/null and b/img/pbaa_logo_transparent.png differ