Bioinformatics


Bioinformatics Collaborations and Services

The NCGR Informatics group delivers advanced, comprehensive bioinformatics analytics and interpretation. We offer a suite of standard analytical packages, but are particularly interested in forming collaborations through which we can develop novel methods and pipelines that leverage our strengths, especially in the area of applying PacBio long read technology to challenging genome assembly projects. Our team has developed several methodologies and pipelines for various aspects of sequence analysis. We have a broad and diverse experience in analyzing sequence data ranging from prokaryotes to complex eukaryotes, including humans and several plant and animals. Please contact This email address is being protected from spambots. You need JavaScript enabled to view it. to discover how we can help move your research forward.

Standard Services:

  • Genome and Transcriptome SNP and Small Indel Discovery: Alignment of short sequence read data to a genome and transcriptome reference to predict single nucleotide polymorphisms (SNPs) and indels.
  • RNA-Seq Expression Analysis: Alignment of RNA sequencing reads to a genome or transcriptome reference, read-count based expression and differential expression reports.
  • De novo Transcript Assembly and Annotation: De Bruijn graph based transcriptome assembly with annotation of predicted peptides using protein motif databases.

Collaborative Work and Custom Assistance:

  • Project planning & experimental design assistance
  • Quality validation and data pre-processing
  • Analysis of data from the major sequencing platforms
  • Collaborations on grants and contracts
  • Improving genomic assembly projects using PacBio long reads
  • Hybrid short/long read genome assemblies
  • Pure PacBio long read genome assemblies
  • Epigenomics analysis
  • ChIP seq analysis
  • Small RNA analysis

 

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