R3 Test Set

Overview

• 42 HPRC (Year 2) samples
• Comprehensive sequencing data, including both trio and Hi-C for all samples
• ONT data on both R9 and R10 flow cells, provided in separate index files:
  • R3_data_index_testset-ont_r9.csv
  • R3_data_index_testset-ont_r10.csv
  • Please Note: only Y1-Y3 samples will have double ONT coverage (R9+R10). Y4-Y5 samples will only have R10 data, so half the overall coverage of the Y1-Y3 samples.
• DeepConsensus (DC) FastQs lack methylation calls; redundant HiFi BAMs are included for methylation analysis
• R2 assembly locations included for reference
• Finalized dataset: complete and will remain unchanged in Release 3

Purpose

This collection supports development and testing of assembly protocols for Release 3.

Data Access

Google Sheet (interactive browsing):
https://docs.google.com/spreadsheets/d/1H_JePzde0bc_Aq88G8K7Ew6kwfqwlSlE9P8gW7UyFoE/edit?usp=sharing

Documentation

For additional documentation on data types and format see the R2 data repo:
https://github.com/human-pangenomics/hprc_intermediate_assembly/tree/main/data_tables

Contact

Questions? Contact Ivo Violich on T2T #assembly Slack channel or at iviolich@ucsc.edu.