Index of /public/dataset/HiFiTE_Revio/Nov_2022/TwistAllianceDarkGene

Icon  Name                                               Last modified      Size  Description
[PARENTDIR] Parent Directory                                                        -   
[TXT] README.txt                                         2022-11-11 11:59  1.3K  
[TXT] TwistAllianceDarkGenes_GeneList.txt                2022-11-11 11:47  2.3K  
[   ] HG002.GRCh38_noalt.deepvariant.haplotagged.bam.bai 2022-11-08 14:48  3.7M  
[   ] HG001.GRCh38_noalt.deepvariant.haplotagged.bam.bai 2022-11-08 14:49  3.8M  
[   ] HG001.fastq.gz                                     2022-11-08 14:30  1.5G  
[   ] HG002.fastq.gz                                     2022-11-08 14:29  1.6G  
[   ] human_GRCh38_no_alt_analysis_set.fasta             2022-11-08 14:51  2.9G  
[   ] HG001.GRCh38_noalt.deepvariant.haplotagged.bam     2022-11-08 14:33   15G  
[   ] HG002.GRCh38_noalt.deepvariant.haplotagged.bam     2022-11-08 14:37   16G  

OVERVIEW
	PacBio HiFi reads for HG001 (NA12878) and HG002 from target enrichment Twist Alliance Dark Gene Panel.
	2 of the 12 samples sequenced on Revio SMRT cell 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 Dark Genes Panel
	PACBIO LIBRARY 	SMRTbell prep kit 3.0 Prepared according to https://www.pacb.com/wp-content/uploads/Procedure-checklist-Preparing-multiplexed-amplicon-libraries-using-SMRTbell-prep-kit-3.0.pdf
	SEQUENCING	Revio system, 24 hr movie
	ANALYSIS	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
HG001.GRCh38_noalt.deepvariant.haplotagged.bam			aligned HiFi reads, PCR duplicates marked, reads tagged by haplotype (HP tag)
HG002.GRCh38_noalt.deepvariant.haplotagged.bam			aligned HiFi reads, PCR duplicates marked, reads tagged by haplotype (HP tag)
HG001.fastq.gz							demultiplexed HiFi reads
HG002.fastq.gz							demultiplexed HiFi reads
human_GRCh38_no_alt_analysis_set.fasta				reference used to generate BAM files
TwistAllianceDarkGenes_GeneList.txt				gene list