Sanger Sequencing Client Portal

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Sanger Sequencing Client Portal

Purchase eVouchers

Start Sequencing Submission

Whole Genome Sequencing

We provide Whole Genome Sequencing for both large (Mammalian/Plant) and small (Bacterial) genomes, providing advice on the most appropriate library preparation and sequencing platform for your project.

Our service has the flexibility to vary the amount of coverage required to suit the application required – whether that is a shallow depth of sequencing to assess structural variation within the genome, standard depth for genome resequencing or a higher coverage to detect rare SNPs, particularly where these are not covered by targeted approaches.

We can also support DNA extraction requirements upstream of the library preparation from a variety of sample types as well as offering advanced Bio-Informatics to cover the analysis.

Advances in library preparation methods such as Nextera flex provide a fast and reliable library prep workflow from low input amounts whilst PCR free methods are also available.

It is possible to sequence novel organisms and assemble the sequencing data by a de novo assembly, complimenting shorter Illumina reads with long reads, to provide an accurate DNA sequence for a previously unknown organism.

Overview

Sequencing package details

The standard package for higher organisms (human/mouse/rat) includes library preparation of your choice – standard gDNA, low-input or PCR free, sequencing of each sample to ~100Gb of raw data and allows flexibility for deeper coverage with additional units of sequencing depth in 30Gb multiples. This equates to ~30X and ~10X raw data coverage, respectively. For smaller genomes we can tailor our pipeline to offer guaranteed data amounts based on your genome size.

Our standard package offering includes:

  • Initial QC and library preparation
  • Illumina 150bp PE sequencing at 30x coverage (~100Gb data per human genome)
  • Return of raw FastQ files via secure FTP or HDD

Optional extra services available:

  • Additional sequencing depth 
  • DNA Extraction 
  • Bioinformatics analysis 

 

The process

 

whole-genome-sequencing 

We also offer DNA extraction and standardised or bespoke advanced Bio-informatics solutions.

BioInformatics Variant Calling

Germline:

Investigation of germline single nucleotide polymorphisms (SNPs), insertions and deletions (INDELs) present in either whole genome or exome data.

This analysis uses Next Generation Sequencing data to identify any germline mutations by comparison to a reference sequence. Raw reads are trimmed, aligned and deduplicated, followed by variant calling, recalibrating, filtering and finally annotating variants with entries from relevant public databases such as dbSNP and ClinVar. You will receive raw (fastq) and aligned (bam) files for each sample, as well as VCF files listing all variants. A bioinformatics report will provide further detail about the tools used and alignment metrics and a variant quality stats.

Additionally, access to an interactive online viewing tool (Relyter) is available now.

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Somatic:

Identification and quantification of somatic single nucleotide variants (SNVs), insertions and deletions (INDELs).

This analysis uses Next Generation Sequencing data from cancer samples to identify somatic mutations by comparison to either a reference sequence and/or a matched healthy sample. Raw reads are trimmed, aligned, deduplicated and somatic variants are called via local de-novo assembly of haplotypes in active regions. Regions showing signs of somatic variation are then reassembled to generate candidate variant haplotypes. Further steps include contamination calculation, orientation bias detection and finally filtering and functional annotation of variants with databases such as GENCODE and dbSNP. You will receive raw (fastq) and aligned (bam) files for each sample, as well as VCF files listing all variants. A bioinformatics report will provide further detail about the tools used and alignment metrics and a variant quality stats.

How to order

Contact us today and one of our skilled account managers will be in touch with a free consultation including further information and pricing details. 

Payment options:

Payment can be made by credit card or purchase order number.

FAQ's:

View our frequently asked questions for more information. 

Sample requirements:

We require 1-2 ug of gDNA (0D260/280 ratio ranging from 1.8-2) at a minimum concentration of 50ng/ul and in a minimum volume of 20ul. Higher concentrations can be submitted and will be diluted accordingly. For full details click here.