Whole Genome Sequencing – Genetic Resources Core Facility, Johns Hopkins University, School of Medicine

Whole Genome Sequencing

The GRCF High Throughput Sequencing Center now offers whole genome sequencing on the NovaSeq 6000.

Human genome sequencing at 30x average coverage, from short-insert paired-end reads using a single library.


Sample Requirements	Input DNA amount: 1ug high molecular weight genomic DNA for PCR free (preferred), 500ng for PCR based methods
Deliverables	Genomic coverage at a minimum of 30x GATK best practice called sequence variants: (SNPS, CNV’s, small indel) multisample calling (if applicable) Annotation of SNPs and indels in VCF format (dbSNP, gene, exon, transcript) Concordance with whole-genome genotyping arrays Raw data (reads and quality scores) and analyzed data in industry-standard format (archival BAM)
Pricing	$1500/genome, highly dependent upon sample number

10X linked read whole genome sequencing at 30x average coverage, from 10X GemCode library, short-insert paired-end reads.


Sample Requirements	Input DNA amount: 1.2ng high molecular weight genomic DNA (>50Kb minimum)
Deliverables	Genomic coverage at a minimum of 30x Whole Genome Phasing and SV calling via 10X Longranger Pipeline SNP/short indel calls using GATK/Freebayes Concordance with whole-genome genotyping arrays Annotation of SNPs and indels in VCF format (dbSNP, gene, exon, transcript) Raw data (reads and quality scores) and analyzed data in industry-standard format (archival BAM). Loupe browser file
Pricing	$3000/genome, highly dependent upon sample number

We also offer de novo whole genome assembly using 10X linked reads. Please inquire if interested, as pricing depends on genome size and complexity.