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Whole Genome Sequencing

Whole Genome Sequencing
Use whole genome sequencing to:
  • Detect single nucleotide to large structural variations in your model organism
  • Detect off target mutations of your CRISPR/Cas9 gene editing experiment
  • validate your bacterial production strain
  • characterize microbial isolates by MLST



Considerations before starting a whole genome sequencing project:

  • Scientific objective
  • Availbility and quality of a reference genome
  • SNV detection and/or SV detection
  • Optimal coverage/sequencing depth & read length
  • Are substantial DNA contaminations suspected

Let us guide you – from design to analysis

Example projects using whole genome sequencing:

  • Detection of mutations aquired by cancer cells – from SNPs to large structural variations
  • Insertion site detection
  • Mutation verification, ruling out off-target mutations
  • Genetic modifications in breeding studies

Applications related to whole genome sequencing:

  • RNA Sequencing
  • Whole exome resequencing


A typical workflow for a eukaryotic resequencing project is shown in the graphic below. Please note that our highly-modular processes allow you various entry and opting out options. If you outsource your entire NGS project to Microsynth or only parts of it is up to you.
For further reading and a detailed technical description, please download our Application Note Eukaryotic Resequencing (see related downloads).


Without Bioinformatics

Raw data:

If no analysis module is ordered, Microsynth provides for Whole Genome Sequencing the key outcomes as listed below:

  • Assessment of Sequencing Quantity and Quality(in .xlsx format)
  • The evaluation of the quantity and quality of the sequencing data.
  • Raw data ( per sample, in .fastq format)
  • The raw data allows you to run your own analysis or track back to each nucleotide sequenced.
  • A Project summary report(.pdf format)
  • The report summarises the key Parameters of the Project.

With Bioinformatics

Standard Bioinformatic Analysis:

For our resequencing application, in addition to the raw data, Microsynth's analysis module provides a variety of insights to meet your scientific objectives:

  • Sequencing Quantity and Quality Evaluation (in .xlsx and .html format)
    A comprehensive assessment of sequencing quantity and quality, providing crucial insights.
  • Alignment/Map Files and Indexes (in .bam and .bai format)
    Access alignment and map files along with their corresponding indexes for your convenience.
  • Genome Coverage and Read Depth Analysis(in .tsv and .bed format; see Figure 1)
    Gain insights into genome coverage and read depth through results provided in .tsv and .bed formats.
  • Structual variations & Copy number analysis (compare Table 1 & Figure 2)
  • Variant Calling of SNVs and small InDels (in .vcf format, see Table 2 and Table 3 )
    Identify single nucleotide variants (SNVs) and small insertions/deletions (InDels < 50 bp) with variant calling results available in .vcf format.
  • Annotation of Variations with Amino Acid-Level Consequences (in .html format, see Table 4)
    Understand variations with potential amino acid-level consequences, presented in .html format (accessible for most model organisms/if the reference genome is annotated accordingly).


  • Filtering of Variants Against a Background Sample (in .html format)
    Customize your analysis by filtering variants against a background sample, with results provided in .html format.
  • Sample Consensus Sequence (in .fasta and .gb format)
    Receive a sample consensus sequence, potentially resulting in a chimeric sequence, in .fasta and .gb formats.


Complementary Bioinformatic Analysis (at additional cost)

Genomic Epidemiology (for prokaryotes only):

  • Screening for matches to resistance and virulence databases and mycotoxin genes (in .tsv format)
    Identify matches to resistance and virulence databases with screening results provided in .tsv format.
  • Phylogenetic Typing of Sample Strain (in .pdf format)
    Understand the phylogenetic relationship of your sample strain through a concise .pdf report.

These results empower you with a comprehensive view of your re-sequencing analysis, enabling you to extract meaningful insights and make informed decisions.


Figure 1: Genome coverage histogram.

Table 1: This detail of a result table shows detected single nucleotide variations, small insertions and deletions and their annotation.

Table 2: Summary table for observed SNVs and InDels in the analyzed samples including the type of mutation (silent vs. non-silent). Differences in numbers are due to variations in non-coding or not annotated genomic regions or already reported isoforms.

Table 3: This detail of a result table lists putative structural variations.

Figure 2: This figure depicts a possible copy number variation in relation to a reference sample.

Table 4: Table displaying detailed information on each observed variation like variant type and position, affected protein including reference and altered sequence.

Turnaround Time

  • Delivery of data within 20 working days upon sample receipt (includes library preparation and sequencing)
  • Additional 10 working days for data analysis (bioinformatics)
  • Express service possible on request