Contact Information

Primary Contact

Alice Young
Group Director


5625 Fishers Lane
Room 5S-16
Rockville, MD 20852


NISC’s role within NHGRI, and more broadly across NIH, aims to advance genome sequencing and its many applications, with a goal not simply to produce sequence data, but to produce the infrastructure required to bring genomic sequence to biology and medicine. We accomplish this by meeting with each NIH investigator to discuss the details of their project to determine which method(s) would work best. The most common types of sequencing projects include whole exome sequencing, RNA sequencing, custom capture sequencing, CHiP-seq and whole genome sequencing. However, we are always interested in exploring new methods and expanding our repertoire in this rapidly changing field. We also work closely with other investigators across the NHGRI Intramural Research Program to develop novel methods to analyze genomics data with applicability to clinical and basic science questions that were thought to be intractable only a few years ago.

List of Services

  • Whole Exome Sequencing and AnalysisFAQ
  • Bulk RNA-SeqFAQ
  • Single-Cell RNA-SeqFAQ
  • ChIP-SeqFAQ
  • Whole genome sequencing (Eukaryotic and microbial)FAQ
  • Amplicon sequencing
  • Custom capture projectsFAQ
  • Library Construction – NISC has a highly skilled library construction group able to make a wide range of libraries compatible with all of our sequencing platforms. You deliver high-quality DNA or RNA and we construct the library. We prefer to start a sequencing project at this point, which allows our experienced hands to control each step for optimal performance and ensure the highest rate of success at the end.
  • Data Return – The raw data from the sequencers is extensively processed, and data is evaluated for quality. For Illumina data, the general deliverable is fastq files which contain the base calls as well as sequence quality scores.
  • Exome Analysis – NISC provides data analysis for all human whole exome and custom capture sequencing projects. Variants, genotypes, and annotations are delivered to the investigator in tab-delimited format compatible with VarSifter, a java-based genotype viewer, available from NISC. We hope to provide this analysis for human whole genome sequencing projects in the near future.

Major Instrumentation

  • Illumina NovaSeq 6000 - The NovaSeq 6000 offers scalable sequencing through multiple flow cell modules. The most cost-effective module is the S4 which produces ~2.5 Tb per flow cell or ~ 625 Gb per lane. Due to the extremely high quantity of sequence output, this technology is primarily useful for projects requiring a very large number of reads, such as whole genome, whole exome and multiplexed transcriptome experiments. 
  • Illumina NextSeq 550 - The NextSeq 550 is a mid-range output sequencer. Multiple run options are offered, with outputs ranging from 16 Gb to 120 Gb and read lengths from 1 × 75 b to 2 × 150 b. This platform is ideal for smaller projects or those requiring non-standard run conditions, such as single-cell RNA-Seq. 
  • Illumina MiSeq - MiSeq is a small-scale benchtop sequencer. This instrument is compatible with any of the Illumina libraries described above. MiSeq produces reads up to 300 bases in length from a paired-end read run (2×300 b) with a yield of ~10 Gb. This capability is primarily useful for sequencing microbial genomes and amplicons. 
  • PacBio Sequel II - The PacBio Sequel II platform generates long read lengths while maintaining high consensus accuracy and unbiased coverage. The maximum read length is more than 50 kb and high fidelity (HiFi) reads >10 kb with >99.9% accuracy can also be generated. This platform can generate sequence reads that support high-quality assemblies from small bacterial genomes all the way up to diploid human genomes. Other applications include amplicons, full length 16s sequencing, epigenomes, and RNA isoforms. For most applications one SMRT cell generates 20-50 Gb of data and completes in 20-30 hours. 
  • Oxford Nanopore GridION and PromethION - The Oxford Nanopore platform is the newest and most rapidly evolving platform in our portfolio of sequencing technologies. Monitoring current fluctuations as native DNA or RNA molecules pass through nanopores, this approach has key advantages of being able to read ultra-long fragments (some > 1Mb) and detecting modified bases without special library construction. Base calling is done in real time making sequence data available right from the start of the run. Raw read accuracy is currently about 98% with new advances expected to push that over 99%. The primary uses of this technology to date at NISC have taken advantage of the ultra-long reads to detect large structural variants and create de novo genome assemblies. Using this approach, a typical PromethION flowcells yields 80 Gbase of quality reads with N50 approximately 72kb. Preliminary experiments have also been undertaken to explore direct RNA and full-length cDNA sequencing.

User Guidelines

The NIH Intramural Sequencing Center provides cost-recovery sequencing services to the NIH Intramural Community. Initiating A Project – If you are thinking about initiating a new sequencing project, please visit After this form is submitted, we will set up a meeting with you to plan the best approach for your needs. Please note that our sequencing service is restricted to intramural investigators at the NIH. Human DNA samples will need to be properly consented and de-identified.