bioinformatics-sc

Flexible bioinformatics solutions for all experience levels

We understand that all analyses are different and thus we offer a variety of data analysis services. Whether you are new to next-generation sequencing (NGS) or just lack experience with a particular application, our data analysis options can help you get the most out of your data.

Data analysis services

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Consultation with customer

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Customer submits data

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Bioinformatics specialist performs data analysis

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Review results with customers

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Conclusions and future plans

Our experienced bioinformatics specialists can help with virtually any type of data analysis related to NGS. All of these services can be customized depending on your requirements. The number of hours required for your project, specific objectives, and defined deliverables will be estimated during the initial consultation.†

Each data analysis service begins with a consultation with one of our experienced NGS bioinformatics specialists in order to understand your specific requirements and define the scope of work required. During the consultation we determine the project deliverables and project timeline.† Next, you submit your data (usually SFF or BAM files via FTP, or on an external hard drive). We then analyze your data using our state-of-the art computing environment, which includes use of our innovative Ion Reporter™ Software, as well as Ingenuity® and other third-party analysis tools when appropriate.

At the conclusion of the project, the bioinformatics specialist assigned to your project reviews the results with you and helps you understand the full biological significance of your data. Data review can occur via a virtual meeting or on site* at your facility.

Jump-start your Ion Torrent™ data analysis capabilities. Contact us to discuss your project and we’ll help you decide on the most cost effective option for your situation, whether it be on an hourly consulting basis or as part of our Bioinformatics Services Packages.

This service may include:

  • Setting up your Ion Torrent™ Server
  • Configuring your Ion Torrent™ Server data management strategy
  • Configuring Ion Torrent™-supported plugins
  • Consultation on Ion PGM™ and Ion Proton™ systems and a data analysis overview
  • Selecting adequate primary data analysis workflow parameters
  • Optimizing your Ion Torrent™ browser and secondary analysis parameters
  • Setting up Integrative Genomics Viewer (IGV) for viewing alignment results
  • Demonstrating Ion Torrent™ System maintenance and updates
  • Using Ion Ampliseq™ Designer
  • Configuring Ion Reporter™ Software to operate seamlessly with Ion Torrent™ Server output
  • Transferring runs to the Ion Reporter™ Server System

Get the desired balance between sensitivity and specificity on variant output from Ion Torrent™ Variant Caller (TVC). There are many nuances to variant calling in NGS data. The goal of this service is to reduce the time you spend manually filtering through variants by optimizing the variant calling pipeline and customizing variant caller parameters for your specific application.

For customers with control samples with known variants, our experienced bioinformaticians can help improve your false positive to false negative ratio or target increased sensitivity on specific variants of choice. The optimization path includes analysis of TVC run output for a specific application, adjustment of advanced parameters in the caller, and customization of the TVC calls within your TS. Additional steps can be taken to optimize your Ion Reporter™ software reporting path and appropriate customization of output reports. Our workflow optimization service may include:

  • Analyzing the current ROC curve in your own application [given gold-standard data set(s)]
  • Selecting desired parameter settings
  • Streamlining the application of agreed-upon parameters throughout project
  • Customizing Ion Reporter™ filters, annotations, and reports

Whether you're new to next-generation sequencing or a seasoned expert, we can help you get the data you need from your RNA-Seq experiment. We'll work with you to define your experimental parameters to meet your data analysis parameters, including:

  • Choosing species of RNA to interrogate
  • Assessing the integrity of total RNA and performing pre-alignment QC
  • Setting up controls, normalization, replicates, and references
  • Anticipating the amount of data or number of samples per chip
  • Optimizing statistical, SNP, and GeneSet analysis
  • Using open source or commercial software
  • Setting up an effective IT infrastructure

Develop a clear path for your Ion Torrent™ RNA-Seq data analysis. Take the guesswork out of performing RNA Ion AmpliSeq™ Design or Torrent Suite™ RNA-Seq and RNA-panel analysis. Determine which additional plugins or third-party software are the best fit for your application and site needs. Our in-house bioinformaticians will guide you through a range of activities related to Ion AmpliSeq™ RNA or RNA-Seq data analysis. This consultation service may include:

  • Setting up custom Ion AmpliSeq™ RNA Design
  • Troubleshooting Ion AmpliSeq™ Designer output
  • Configuring Ion AmpliSeq™ data analysis workflows
  • Configuring the appropriate reference files for Ion Torrent™ Server
  • Checking sample quality with the Coverage Analysis Plugin and the Coverage Analysis Plugin Lite
  • Fixing custom design problems
  • Discussing tertiary analysis tools for downstream analysis, either free or from third parties

Written agreement required.
*Additional travel and accommodation charges may apply for meetings held on site at customer’s facility.