Archive by Author | Raymond Tecotzky

BaseSpace 2015 WWDC @ The Broad



Space is limited, so please register early.

Create your own Apps in BaseSpace!

Publish your favorite novel algorithms or applications on BaseSpace.

At this free event, you will learn how to build and launch your own bioinformatics Apps in BaseSpace.
Make an impact on the analysis and interpretation of genomic information by publishing your own BaseSpace App!

Friday, April 24, 8:00 AM to 5:00 PM |  The Broad Institute

415 Main Street Cambridge, MA 02142 | Monadnock Meeting Room, 2nd Floor

Who should attend?

● Engineers
● Researchers
● Software Developers with a focus in Bioinformatics
● Managers
● Academics
● Statisticians
● Computational biology and chemistry professionals
● Biopharma industry professionals
● Commercial Bioinformatics professionals


Space is limited, so please register early.

DeepChek®-HIV – App for genotyping by NGS and inferred drug resistance testing – for research use only



HIV genotyping and inferred drug resistance testing has become an integral part of the clinical management of patients infected with HIV. Detecting minority populations of resistant viruses is now routinely done. Next-generation sequencing (NGS) technology is replacing  Sanger sequencing methodology, and end-to-end solutions combining sensitive genomic tests with advanced data management software platforms are in high demand.

DeepChek®-HIV is easy-to-use downstream analysis software for NGS data management, interpretation, and reporting for Research Use Only. DeepChek is a reliable software and database solution that is capable of handling the complexity of NGS data for all the key genomic regions involved in HIV drug resistance (reverse transcriptase, protease, integrase, GP41, and GP120/V3). The database is regularly updated with the most recent drug resistance information and provides an efficient and downstream analysis platform for clinical laboratories involved in routine HIV-1 genotyping and drug resistance testing.


Link to App in BaseSpace: 


Link to example dataset with example input data and output results:



Introducing VariantStudio on BaseSpace

VariantStudio v2.2

Sequence and stream data to BaseSpace- done.  Run quality check- done.  Alignment and variant calling- done.  Congratulations, you now have a set of variants!  But what good is a set of variants if you can’t describe what they mean, how they might explain the phenotype of the specimen, and which ones aren’t worth worrying about? There is good news- now that Illumina VariantStudio is available on BaseSpace, deciphering the biological meaning of genomic variants is not a huge challenge.  If you’re not familiar with it, VariantStudio1 is an easy-to-use tool for variant annotation, filtering, and reporting.

  • Step 1: Import data into VariantStudio. Click the import button and you will be able to browse and select VCF and gVCF files stored in BaseSpace to import into VariantStudio.  You can import DNA variant data from targeted, exome, or whole-genome sequencing, but VariantStudio only supports human SNP and indel analysis at this time.
  • Step 2: Annotate variants using the Illumina Annotation Service, which aggregates annotations from a broad range of public sources including ClinVar, COSMIC, OMIM, and 1000 Genomes Project. Variants will be richly annotated with biological information including transcript consequence, functional impact, known disease association, population allele frequency, and more.
  • Step 3:  Apply a cascade of filtering options to quickly create a short list of candidate variants that are likely associated with the disease or phenotype. In addition to single sample analysis, you can perform tumor/normal comparisons to identify somatic mutations or family-based analyses to investigate variants underlying rare disease.
  • Step 4: Use the provided annotations to classify variants based on their presumed biological impact. A common scheme is pathogenic, likely pathogenic, benign, or unknown significance. Or you can use your own, customizable classification scheme.
  • Step 5:  Generate a customizable report that summarizes your important variants, along with any additional metadata.

Import variants > Annotate > Filter > Classify and Interpret > Generate Report.  Watch our analysis videos and see how quickly you can go through this workflow. VariantStudio is a powerful, secure2  tool to simplify genomic data interpretation, and accessing it on BaseSpace is  just a click away.  With the addition of VariantStudio to the BaseSpace Core Apps, BaseSpace users can now execute the entire sample-to-answer workflow- from generating sequence reads to reporting biologically significant results.

Related Information:

1. datasheet_illumina_variantstudio_software.pdf

2. technote_variantstudio_data_security.pdf