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      Human Whole-Genome Sequencing, HG002 (GIAB), PCR-free WGS, VITARI™, 2×151 sequencing

      Background

      PCR-free whole-genome sequencing (WGS) libraries from GIAB reference sample HG002 (NIST NA24385) were sequenced on Element VITARI. For each of two independent runs, demultiplexed HG002 FASTQs from a single lane are provided at full lane depth and as a random downsample to approximately 35× coverage.

      Dataset summary

        VITARI-0965 VITARI-0966
      Sample ID VITARI-HG002-L044
      		 VITARI-HG002-L044
      Sample HG002 (GIAB / NIST NA24385) HG002 (GIAB / NIST NA24385)
      Library PCR-free WGS PCR-free WGS
      Platform / chemistry VITARI, Cloudbreak Freestyle VITARI, Cloudbreak Freestyle
      Read length 2×151 (I1/I2 = 8) 2×151 (I1/I2 = 8)
      Lane Lane 4 Lane 4
      Full-lane HG002 FASTQ VITARI-HG002-L044_R{1,2}.fastq.gz (~914M read pairs) VITARI-HG002-L044_R{1,2}.fastq.gz (~857M read pairs)
      35× HG002 FASTQ VITARI-HG002-L044_FQD-2x150x150-35x_R{1,2}.fastq.gz (~360M read pairs kept; random downsample, seed 0; 2×150; ~35×) VITARI-HG002-L044_FQD-2x150x150-35x_R{1,2}.fastq.gz (~360M read pairs kept; random downsample, seed 0; 2×150; ~35×)

      Methods

      PCR-free WGS libraries were prepared from HG002 genomic DNA and sequenced on VITARI using Cloudbreak Freestyle™ chemistry (300-cycle kit; R1/R2 = 151 cycles, I1/I2 = 8 cycles). HG002 was sequenced on lane 4 of two independent runs (VITARI-0965 and VITARI-0966).

      Bases2Fastq was used to generate FASTQ files for GIAB HG002 with sample ID VITARI-HG002-L044 (VITARI-HG002-L044_R1.fastq.gz / VITARI-HG002-L044_R2.fastq.gz). For convenience, and to match the inputs used in Element’s secondary-analysis benchmarks, each full-lane FASTQ was randomly downsampled to approximately 35× coverage (2×150; fixed seed), producing VITARI-HG002-L044_FQD-2x150x150-35x_R1.fastq.gz / VITARI-HG002-L044_FQD-2x150x150-35x_R2.fastq.gz.

      The 35× FASTQs were processed with (1) vg giraffe (v1.67.0) on the HPRC v1.1 GRCh38 graph followed by DeepVariant pangenome-aware 1.10.0, and (2) Sentieon CLI pangenome (sentieon-cli-nf 1.2.0 / Sentieon CLI 1.6.2 on HPRC v2.1) using the Element Biosciences pangenome WGS model 1.0. Small-variant accuracy was evaluated against GIAB HG002 v5.0q (GRCh38).

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