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Whole Genome Sequencing (WGS)

Whole Genome Sequencing (WGS) provides the most comprehensive map of an organism’s genetic make-up. Unlike targeted or exome sequencing, WGS covers all corners of an organisms’ entire genome, which is arguably the most important molecular data. For bacteria, this approach is highly effective for studying virulence, drug resistance or novel drug targets.

Similarly, comparative genomic for eukaryotes through resequencing or de novo assembly is the best approach to obtain high resolution genomic variations. High quality sequencing is now available with as little as 1 ng of starting material.

Key features for WGS service

  • Sequencing Platform
    • Illumina
  • Starting Material
    • 50 ng (eukaryote) or 1 ng (prokaryote)
  • Sequencing Type
    • 75 bp paired end
    • Longer read lengths available upon customer request
  • Library Type
    • 500bp fragment size (average)
    • Larger fragment size available upon customer request
  • Bioinformatics Analyses
    • Read alignment
    • SNP and Indel calling
    • de novo assembly*
    • Unified genomic variation detection*
  • Turn-around Time
    • 2-4 weeks for sequencing plus 2-3 weeks for analysis
  • Data Storage
    • 3 months

*Offered with a minimum of 100X coverage

Exploratory Bioinformatics Analyses

Unified Variation Caller detects genomic variation using an alignment-based and de novo assembly-based approach that is more sensitive and accurate in comparison to many popular choices such as VarScan, Pindel, and GATK. Our key advantage is the ability to accurately detect compound variations (deletions and insertions occurring at the same loci).

High quality assembly enables accurate calling of SNPs, Simple Indels, and large Compound Variations. Circos plot (right) shows from outside to inside: Reference genome (brown), SNP density (green), Simple Deletion size (blue), Simple Insertion size (red), Compound Variation size (grey). 

Deliverables

  1. Sequencing results in FASTQ format
  2. SNP and Indel calling
  3. Contig and scaffold sequences from de novo assemblies in FASTA format (if applicable)
  4. QC and analysis report

All of Microgem’s sequencing services are performed by a group of specially trained and experienced scientists partaking in a streamlined workflow.