Supported by CCR Office of Science and Technology Resources (OSTR)

Bioinformatics

Bioinformatics Support at Frederick Sequencing :

The NGS Group uses high-throughput sequencing technologies to enrich cancer research and ensure that the NCI community can remain at the leading edge of NGS. Since its inception in 2009, NGS Group Bioinformatics group (CCR-SF IFX) provides a broad range of bioinformatics support services to CCR investigators and their collaborators. Our team has diverse expertise in bioinformatics pipeline development and NGS data analysis support. Our mission is to provide the highest quality of sequencing data to our customers.  We work closely with investigators to help get their NGS projects off the ground.

Requests for Bioinformatics support should be discussed during the sequencing project consultation. Please contact Yongmei Zhao (yongmei.zhao@nih.gov, 301-360-3455) or CCRSF_IFX@nih.gov for any assistance.

Main Area of Support:

  • Project Consultation – we offer experimental design consultation including sequencing technology recommendation, library protocol consultation, sequencing coverage and cost estimate, etc. Proper consultation ensures our customers receive the best sequencing strategy for their project with most cost-effective manner.
  • Data Analysis & Interpretation – we perform QC, secondary and tertiary data analysis based on application types for sequencing data generated from Illumina, PacBio, Oxford Nanopore, as well as single cell technologies.
  • Bioinformatics Research and Development – we develop robust and reproducible analysis workflows and pipelines based on application types and sequencing technologies. We share our software pipelines through open-source platforms such as GITHUB (https://github.com/CCRSF-IFX). 
  • Collaboration – we work closely with NGS Group laboratory scientists, support adaptive new sequencing protocols and new technology development. We provide customized data analysis through the development or adoption of new bioinformatics workflows. We actively engage with scientific communities for development best practices in NGS quality control, benchmark bioinformatics methods, NGS protocols and sequencing technologies.
  • Data Management – we perform data management of all NGS data generated at NGS Group and provide investigators easy access to their sequencing project data and analysis results using the High-Performance Computing Data Management Environment (HPC DME) system. We help investigators to submit their sequencing project data to public databases.
  • Bioinformatics Training – We provide training to customers for NGS technology and data analysis. We offer advice regarding tools and methods suitable for further analysis and result interpretation.

Analysis Services:

  • Transcriptome Analysis – support both short-read using Illumina RNA-seq and long-read using PacBio and Oxford Nanopore platforms for full length transcripts and novel splice variants discoveries.
  • Whole Genome Sequencing Analysis – utilize both short- and long-reads technologies such as Illumina, PacBio, Oxford Nanopore, to detect variations or rearrangements in the structure of chromosomes as well as copy number variations.
  • Whole Genome Methylation Analysis – support the analysis of 5mC and 5hmC using protocols for Illumina short-read sequencing, DNA base modification detection via PacBio Single Molecule Real Time (SMRT) sequencing (including 5mC and both endogenous and exogenous m6A-marked bases), along with direct DNA and RNA base modifications (4mC, 5mC, 5hmC, 6mA in DNA, and m6A in RNA) using Oxford Nanopore sequencing.
  • Targeted Sequencing Analysis – utilize adaptive sampling of Oxford Nanopore technology to enrich or deplete any regions of the interest (ROI) in genome to get the high quality and efficient coverage of the ROI; PacBio targeted RNA Iso-seq using hybridization capture to enrich full-length transcripts of interests; utilize Xdrop Sort for whole genome structure variation detection or viral integration site detection.
  • Single cell Analysis – support both whole transcriptome and droplet-based single cell technologies such as 10X Genomics, Fluent Biosciences PIPseq, Scale Bio single-cell RNA sequencing, single-cell multi-omics (targeted DNA, DNA+Protein) analysis using Mission Bio Tapestri platform; spatial transcriptomics technologies such as 10X Genomics Visium, Curio Bioscience Curio Seeker. Additionally, we provide analysis support for PacBio MAS-Seq or Oxford Nanopore for sequencing of full-length transcripts from 10X Genomics single cell captures.
  • 16S amplicon analysis – utilize PacBio SMRT long-read technology to sequence the entire 16S rRNA gene in one read.