High-Throughput Sequencing Initiative Facilities

MiSeq     QIACube

The IFSH High-Throughput Sequencing Initiative or IHI is one of the newest enterprises in IFSH to provide the latest technology for the researchers especially in the food industry. The high-throughput or next-generation sequencing (HTS/NGS) has revolutionized many scientific fields from environmental to human health sciences. The adoption and increased use of the HTS technology and its many applications by the regulatory and health agencies in the US and around the world has begun an inevitable transitional period in our food safety regimes from the old means to the new ones. With unprecedented resolution, the HTS methods and technology enable the researchers and safety personnel in the food industry to examine the products, processes and the environments with an unparalleled power to ensure the best safety measures. The IHI offers HTS Laboratory and analytical services to all especially our colleagues in the food companies.


Two Illumina MiSeq sequencers and one Oxford Nanopore MinIon sequencer that us to provide the following laboratory services:

  • DNA and RNA extraction, purification and quantification
  • Library preparation
  • Whole genome sequencing (WGS)
  • Complete genome sequencing or closing the bacterial genomes
  • RNA sequencing (RNA-Seq)
  • Metagenomics (massive 16s rDNA sequencing)
  • Metagenomics (Shotgun sequencing)

IHI is also housing our state of the art bioinformatics facility, equipped with three high-performance computers (HPCs) with impressive computational power and capability that allow us and our collaborators/clients to process large amounts of data that these sequencing machines produce. Currently our bioinformatics facility provides the below analytical services:

High Performance Computing Equipment for HTS Initiative    High Performance Computing Equipment for HTS Initiative

  • Data storage and remote access
  • Sequence quality inspection and filtration (quality control)
  • Sequence assembly (WGS, RNA-seq or transcriptomics)
  • Sequence assembly assessments (quality control)
  • Sequence assembly comparisons
  • BLAST search and results
  • Sequence annotation
  • SNP analysis (CFSAN SNP Pipeline or kSNP analysis)
  • Phylogenetic analysis and phylogeny reconstruction, tree visualization

HTS Services And Projects


HTS Symposiums And Presentation Materials

The IHI is also active in educational events and training programs. Since its start in 2016, the IHI has organized the following HTS symposiums:

              A Tutorial and Hands-on Workshop to Help Understand Its Application to Food Safety (May 6-7, 2019)

Key Staff Members And Contact Information 


Research Assistant Professor, Leader of IFSH High Throughput Sequencing, IIT

Renmao Tian

Research Scientist Microbial Genomics, IFSH High-Throughput Sequencing, IIT

Membership Application Process

Business Development / Marketing and Communications
708.563.8278 (office)