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

NameLast modified (UTC)Size
Parent Directory-
HG001.GRCh38_noalt.deepvariant.haplotagged.bam.bai2022-11-08 22:493.8M
HG001.GRCh38_noalt.deepvariant.haplotagged.bam2022-11-08 22:3314.8G
HG001.fastq.gz2022-11-08 22:301.5G
HG002.GRCh38_noalt.deepvariant.haplotagged.bam.bai2022-11-08 22:483.7M
HG002.GRCh38_noalt.deepvariant.haplotagged.bam2022-11-08 22:3715.5G
HG002.fastq.gz2022-11-08 22:291.6G
README.txt2022-11-11 19:591.3K
TwistAllianceDarkGenes_GeneList.txt2022-11-11 19:472.3K
human_GRCh38_no_alt_analysis_set.fasta2022-11-08 22:512.9G
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