title: Whole Genome Sequencing of Genome In A Bottle HG004 Illumina NovaSeq 2x250bp Reads
design: GIAB sample HG004 was sequenced using the NovaSeq 6000 SP Reagent Kit (300 cycles) NV2504309-RGSBS (SbsLotNumber: 20374603) on an Illumina Novaseq 6000 SP flowcell (FlowCellLotNumber: 20373362) with 2x250bp paired end reads at the New York Genome Center. Whole genome sequencing (WGS) libraries were prepared using the Truseq DNA PCR-free Library Preparation Kit in accordance with the manufacturers instructions. Raw reads were aligned to the GRCh38 (ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/GRCh38_reference_genome/GRCh38_full_analysis_set_plus_decoy_hla.fa) reference genome (BWA-mem 0.7.15), duplicate reads were marked (Picard v2.4.1), base scores recalibrated (GATK v3.5) , and indels were realigned (GATK).