README for PureTaregt-RE-SQ2e-8plex
Last Updated 03/11/2024

OVERVIEW
This README file describes the contents in this directory.

This dataset was data generated using the PureTarget repeat expansion panel kit.

The PureTarget repeat expansion libraries were barcoded, sequenced on the Sequel IIe system using Chem Bundle 11.3, and processed with SMRT® Link v13.1


DIRECTORIES AND FILES
	0-run_directory/1_A01 
	Outputs for PureTarget repeat expansion application Sequel IIe. On Sequel IIe systems, the PureTarget repeat expansion application retains low quality CCS reads and retains Kinetics.
	Import m64004e_240201_195518.consensusreadset.xml into SMRT Link v13.1 via Data Managment for visualizing un-demultiplexed datasets Dataset metrics and for Demultiplexing analysis in SMRT Link v13.1
	
	1-demultiplexing
	Demultiplexed dataset outputs. When low quality CCS reads are retained, Demultiplexing is performed automatically in SMRT Link.
	Import m64004e_240201_195518.hifi_reads.consensusreadset.xml into SMRT Link v13.1 via Data Managment for visualizing demultiplexed Dataset metrics and for running secondary analysis using the PureTarget repeat expansion workflow.

	1-analysis
	SMRT Link 13.1 SMRT Analysis outputs from PureTarget repeat expansion application workflow run with default GRCh38 reference and the default PureTarget repeat expansion panel application BED.
	Analysis outputs include per sample and per target coverage plots, genotyped repeat expansion VCF and summary CSV for all samples, and per sample per target TRVZ plots for visualizing methylation and motifs for alleles.
	Please reference the SMRT Link v13.1 User Guide for a full list and description of files.
REAGENTS AND SAMPLES

	Nanobind® HT CBB kit for mammalian cultured cells on the KingFisher Apex system
	PureTarget® repeat expansion panel bundle
	SMRTbell adapter index plate 96A
	Binding kit 3.2 + cleanup beads
	SMRT Cell 8M tray
	Sequel II sequencing kit 2.0


HG001 and HG002 samples were barcoded as follows

bc2089	HG001
bc2090	HG001
bc2091	HG001
bc2092	HG001
bc2093	HG002
bc2094	HG002
bc2095	HG002
bc2096	HG002