The Bioinformatics Core facility, combining molecular biology and computer science, provides a variety of data analysis services on biological data. Recognizing the ever-expanding contributions that next-generation sequencing (NGS) experiments are making to public health and the biological sciences, the Bioinformatics Core provides broad analysis of NGS data. The core’s efforts are primarily focused on prokaryotic and viral sequences. For projects where NGS data analysis will be performed, consultation with core staff prior to samples being sequenced is highly encouraged.

Services and Areas of Expertise

  • Complete NGS data analysis, e.g., quality assessment of data, reference mapping of sequence reads to a genome, SNP (single-nucleotide polymorphism) detection and de novo assembly
  • Multiple sequence alignment and genome level sequence alignment
  • Creation of phylogenetic trees from different data sources
  • Microbiome/Metagenomic analysis
  • Data mining large files of biological data
  • Assistance with finding and using publicly available resources for analysis of large datasets (e.g. open-source software and data)
  • Custom programming in scripting languages (Perl, Python R, etc.)  is available for investigator specific needs
  • For custom tasks that need to be performed repeatedly by a lab, the Core can deploy custom software solutions so that they are available at any computer on the Center’s network

Facilities

  • State-of-the-art computing resources, including Google Cloud compute capabilities with extensive memory and disk storage
  • Software package Qiagen Genomics Workbench (formerly CLC Bio) is available for use by all Wadsworth Center staff
    • Genomics Workbench is capable of performing a variety of computational biology tasks including NGS data analysis
  • A multitude of commonly used open-source software packages are installed on core computers and regularly used by core staff, e.g., BWA, samtools, GATK, IGV, Qiime, etc.

Additional Services

In many cases, the Bioinformatics Core can accommodate special requests and project needs.  Please contact Dr. Bruce for further information. Letters of support can be provided to investigators preparing to submit grant proposals to funding agencies.

 

Program Updates

Chip used in sequencing at Wadsworth Center's Advanced Genomic Technologies Core

Publication Exemplifies the Cross-cutting Work of Wadsworth Center’s Public Health Laboratories and Cores

Some of the work of the cores, such as media preparation, is based on techniques that go back over a hundred years, even to the beginnings of what became the Wadsworth Center. Other Wadsworth Center cores perform high-quality antigen production, sophisticated image analysis and manipulation, and sequencing and bioinformatic analysis that may be completed in hours to days rather than weeks or months, often providing comprehensive assessment of a full bacterial genome.
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