Index of /public/dataset/HiFiTE_SqIIe/Oct_2022/TwistAllianceLongReadPGx

 Name                                   Last modified      Size  Description
 Parent Directory                                            -   
 ref/                                   2022-10-17 14:56    -   
 bam/                                   2022-10-17 14:56    -   
 fastq/                                 2022-10-17 14:53    -   
 README.txt                             2022-11-11 12:01  1.2K  
 TwistAllianceLongReadPGx_GeneList.txt  2022-11-11 11:52  517   

OVERVIEW
	PacBio HiFi reads for pharmacogenomics reference samples from target enrichment Twist Alliance Long Read PGx Panel.
	10 out of 24 samples sequenced on Sequel IIe SMRT Cell 8M are released here.

METHODS
	SHEARING	Covaris g-TUBE to target size of 8kb.
	TWIST LIBRARY	Prepared according to https://www.twistbioscience.com/resources/protocol/long-read-library-preparation-and-standard-hyb-v2-enrichment
			Probes: Twist Alliance Long Read PGx Panel
	PACBIO LIBRARY 	Prepared according to https://www.pacb.com/wp-content/uploads/Procedure-checklist-Preparing-multiplexed-amplicon-libraries-using-SMRTbell-prep-kit-3.0.pdf
	SEQUENCING	Sequel IIe System, 24 hr movie, Sequel II Chemistry 2.0, Binding Kit 3.2
	ANALYSIS	Generate HiFi reads with ccs v6.3.0
			Demultiplex with lima v2.5.0
			Mark PCR Duplicates with pbmarkdups v1.0.2
			Align to GRCh38_no_alt_analysis_set with pbmm2 v1.7.0
			Call variants with pbsv v2.8 and DeepVariant v1.4.0
			Phase with whatshap 1.1

FILE DESCRIPTION
bam					per sample aligned HiFi reads, PCR duplicates marked, reads tagged by haplotype (HP tag)
fastq					demultiplexed HiFi reads for each sample
ref					GRCh38 reference used to generate BAM files
TwistAllianceLongReadPGx_GeneList.txt	gene list