Pathogen Sequencing

Pathogen Sequencing

Generate valuable sequencing data for viral and bacterial pathogens from their native environments with myBaits® Target Capture kits.


Overcoming Challenges of Microbial Genome Sequencing

Next-generation sequencing (NGS) is a powerful method for rapid whole-genome sequencing of microbial genomes or overall microbial species content in complex samples. However, most biological samples with microbes of interest are dominated by non-microbial DNA. This necessitates extremely deep sequencing of in order to accurately resolve microbial genomes, or to fully characterize the variation within microbial communities. Targeted sequencing, wherein background non-target DNA is excluded from samples prior to sequencing, solves this problem and drastically reduces the overall costs of sequencing and data analysis per sample. Hybridization capture with myBaits® Target Capture kits is currently the most versatile technique currently for comprehensive,  cost-effective sequencing both viruses and bacteria in complex samples.


Utilize Hybridization-based capture to:

  • Generate whole genome sequences of viruses and bacteria
  • Achieve >100-fold enrichment of pathogens from blood samples
  • Deliver significant sequencing savings by removing host DNA


Hybridization capture tolerates both rearrangements and sequence variation. Both hyb cap and amplicon sequencing can effectively enrich for known sequence regions. However, only hyb cap can retrieve target sequences that have significant rearrangements or mutations relative to the reference used for probe design, such as when capturing genomic content from novel viral strain genomes.


Download  the Targeted Pathogen Genomics via NGS Hybridization Capture application note to apply to your research.

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Feature Publications

Forth, J.H. et al. 2019. A Deep-Sequencing Workflow for the Fast and Efficient Generation of High-Quality African Swine Fever Virus Whole-Genome Sequences. Viruses.

Trimpert, J. et al. 2019. A proofreading-impaired herpesvirus generates populations with quasispecies-like structure. Nature Microbiology. 

Burrell, S. et al. 2017. Ancient Recombination Events between Human Herpes Simplex Viruses. Molecular Biology and Evolution. 

Vezzulli, L. et al. 2017. Whole-Genome Enrichment Provides Deep Insights into Vibrio cholerae Metagenome from an African River. Microbial Ecology.

Campana, M.G. et al. 2016. Simultaneous identification of host, ectoparasite and pathogen DNA via in‐solution capture. Molecular Ecology Resources.

Duggan, A.T. et al. 2016. 17th Century Variola Virus Reveals the Recent History of Smallpox. Current Biology.

Pathogen Panels

Create custom NGS panels for any pathogen or combination, including:

  • DNA Viruses
  • RNA Viruses
  • Bacterial Species
  • Fungal Pathogens

Learn More >>

If you need assistance placing an order, requesting a quote, or technical support, feel free to contact our team directly.
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