Index of /public/dataset/pbAmpliconAnalysis_CYP2D6

Icon  Name                        Last modified      Size  Description
[PARENTDIR] Parent Directory                                 -   
[DIR] workflow_outputs/           2022-04-07 10:18    -   
[DIR] workflow_inputs/            2022-03-14 15:31    -   
[   ] eP138_Harting_ACMG_2022.pdf 2022-03-14 15:40  1.1M  
[TXT] README.txt                  2022-03-14 15:34  1.6K  

********************
INTRODUCTION
********************

   This README file describes the contents in this directory.

   This dataset contains pooled HiFi reads, demulxitpled HiFi reads, and clustered consensus sequences for 
amplicons of CYP2D6 genes for 22 Coriell samples. Amplicons were generated using the
primer design desribed in the included 2022 ACMG poster, and sequence length is approximately 
5kb - 10.1kb. The library was sequenced on the Sequel II system and
processed using the PacBio Amplicon Analysis tool pbAA[1] and the pbCYP2D6 star-typing workflow[2].

********************
SAMPLES
********************

22 genomic DNA samples from Coriell Institute:

NA02016
NA07439
NA09301
NA12244
NA16654
NA16688
NA17020
NA17039
NA17073
NA17114
NA17209
NA17211
NA17214
NA17215
NA17217
NA17226
NA17227
NA17232
NA17244
NA17276
NA17282
NA17300

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METHODS
********************

Library Preparation: 
Amplified using M13-tailed CYP2D6-specific primers described in included poster "eP138_Harting_ACMG_2022.pdf" (see figure 1).

Sequencing: 
Sequel IIe

Run time: 
20hr movie 

Analysis: 
ccs 5.0.0
lima 2.5.0
pbaa 1.0.3
pbCYP2D6typer2 0.2.0

********************
WORKFLOW
********************

See workflow description from included poster and CYP2D6tools github repo[2]. 
Note: Some workflow intermediates (fastq & unpainted aligned HiFi reads) are excluded from this directory.

********************
REFERENCES
********************

[1] PacBio pbAA: https://github.com/PacificBiosciences/pbAA
[2] CYP2D6tools: https://github.com/PacificBiosciences/apps-scripts/tree/master/CYP2D6tools