Whole Genome Sequencing

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

Human Whole Genome

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

Linked Read Whole Genome

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.

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