The CHOP Microbiome Center

CHOP Microbiome Center


The CHOP Microbiome Center is the sequencing resource of the PennCHOP Microbiome Program. The Center is comprised of a Sequencing Core and an Analytical Core. Together we provide end-to-end solutions for microbiome research.

We provide standard fee-for-service and collaborative research arrangements with CHOP, Penn, and external customers

High-throughput Sequencing Core

The Sequencing Core provides expertise in next-generation sequencing of microbiome samples. Services include sample aliquoting, DNA extraction, quantitative PCR, library preparation, and sequencing. All protocols and workflows are optimized for individual sample types.

Infrastructure for deep sequencing includes an Illumina HiSeq 2500 instrument, MiSeq instruments, and Oxford Nanopore technology. The sequencing facility is housed in the Colket Translational Research Building at CHOP. The wet lab is located in the adjoining Abramson Research Center and it includes dedicated pre- and post-PCR spaces. The labs are well equipped with the latest instruments including two automated liquid handling robots for high-throughput processing. The Sequencing Core is staffed by a laboratory manager and three research technicians.

Sequencing Core

Analytical Core

The Analytical Core provides expertise in large-scale bioinformatics analysis of microbiome datasets. Core services start with a thorough quality check and review of sequencing results. This includes removal of host genomic sequences and other DNA added during the sequencing protocol. Automated pipelines assess the bacterial, fungal, and viral taxa found in each sample. Alignments to genes of known function are summarized, and the data are queried against a curated collection of full genomes for microbes of interest.

The primary mission of the Analytical Core is to follow up basic bioinformatics analysis with targeted bioinformatics and statistical approaches that are unique to each study. Rather than applying a one-size-fits-all approach, our goal is to collaborate with other researchers and draw conclusions from the sequence data about which we have high confidence and which reflect the original goals of the experiment.

The Analytical Core is located at the CHOP Roberts Center for Pediatric Research. High capacity network lines connect the Analytical Core to the Sequencing Core, and to the CHOP supercomputing facility in Allentown, PA. The Core is staffed by three full time programmer/analysts and is supported by a network of consulting statisticians.

Analytic Core


Sequencing Queue

Please plan projects in advance. Our queue is currently two months long and we are unable to pre-bill for services.

Turnaround Time

Turnaround time is queue- and project-dependent. Generally, it is 2-3 weeks for 16S projects, 4-6 weeks for shotgun metagenomics projects, and 6-8 weeks for WGS projects. Please let us know in advance if you require a faster turnaround time (special pricing may apply).

Data Guarantee

It is our goal to have each run collect the highest quality and quantity of data possible. Each Illumina NGS platform delivers a maximum output dependent upon the type of flowcell and reagents used. In practice, this output can also be affected by the DNA source and the type of library created.

We guarantee a minimum of 80% of the maximum number of possible reads if we complete all quality control (QC) on submitted DNA and perform the library prep, pooling, and final library QC. All libraries used must pass QC in order for the run to be guaranteed.

We guarantee a minimum of 70% of the maximum number of possible reads if the user submits final library preps generated using CHOP Microbiome Center or standard Illumina protocols and we complete the final library QC. All libraries must pass QC in order for the run to be guaranteed.

We cannot guarantee a minimum data output if custom sequencing/indexing primers are used in replacement of Illumina provided reagents, or if a run includes experimental libraries that have not been previously tested at our Center or by Illumina.

Here are the specifications for the MiSeq and HiSeq 2500 instruments.

For more information, please contact Lisa Mattei (matteil [at] or Jessi Erlichman (erlichman [at]

Request Core Services

The Microbiome Center has now resumed operations. Due to a backlog, we might not be able to start your project immediately, but we are happy to accept new projects and conduct consults. Please fill out our customer request form if you have any upcoming projects that require our services.

Please fill out this form to request pricing or information about our services.

If you have any questions about the application process, please contact us at CHOPmicrobiome [at]


High Throughput Sequencing Core
Abramson Pediatric Research Center
3615 Civic Center Blvd
Room 903F
Philadelphia, PA 19104

Analytical Core
Roberts Center for Pediatric Research
2716 South St
Floor 14
Philadelphia, PA 19146

Request Core Services