Index of /public/dataset/HiFiTE_SqIIe/Oct_2022/TwistAllianceDarkGene

 Name                                                         Last modified      Size  Description
 Parent Directory                                                                  -   
 README.txt                                                   2022-11-11 12:02  1.2K  
 TwistAllianceDarkGenes_GeneList.txt                          2022-11-11 11:47  2.3K  
 NA12878.fastq.gz                                             2022-10-17 14:34  2.6G  
 human_GRCh38_no_alt_analysis_set.fasta                       2022-10-17 08:25  2.9G  
 NA12878_B11_2ul.GRCh38_noalt.deepvariant.haplotagged.bam.bai 2022-10-17 08:15  2.1M  
 NA12878_B11_2ul.GRCh38_noalt.deepvariant.haplotagged.bam     2022-10-17 08:15  2.1G  

OVERVIEW
	PacBio HiFi reads for NA12878 from target enrichment Twist Alliance Dark Gene Panel.
	1 of 4 samples sequenced on Sequel IIe SMRT Cell 8M 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 Dark Genes 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
NA12878_B11_2ul.GRCh38_noalt.deepvariant.haplotagged.bam	aligned HiFi reads, PCR duplicates marked, reads tagged by haplotype (HP tag)
NA12878.fastq.gz						demultiplexed HiFi reads
human_GRCh38_no_alt_analysis_set.fasta				reference used to generate BAM files
TwistAllianceDarkGenes_GeneList.txt				gene list