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Launch GNomEx

Launch Seven Bridges

Launch cBioPortal

We maintain a number of open-source and commercial analysis software on our computing resources. In addition, we also keep copies of publicly available genomic reference sequences, annotation, and alignment indexes. These are available to investigators who have access to our compute resources. See our infrastructure page to learn more about computing resources available.

HCI-Developed Software

Members of the Core have developed custom software applications and tools as part of of our infrastructure service. Many of these are released as open-source code and may be found on our GitHub software repository and include the following:

  • USeq, a collection of over 180 command line java applications for NGS analysis and datatype manipulation. See our USeq page for more information.
  • hciR, comprehensive RNASeq Analysis in R. See our RNASeq page for more information.
  • GNomEx, a genomic data management and visualization web app in use by multiple Utah and national consortia
  • Pysano, a simplified multi-cluster queueing system for submitting jobs to our CHPC nodes.
  • GQuery, a RESTful web app API service for rapidly querying large numbers (> 100K) of genomic data files
  • BioToolBox, a Perl-based general NGS analysis library and toolkit
  • microbiomeSingularityPipeline, a nextflow based microbiome data processing pipeline. See our Microbiome page for more information.

Commercial Software

We have licenses for several commercial software products:

Open-Source Software

This is a partial list of open-source software that we use and maintain on our compute infrastructure.

  • Cohort analysis: cBioPortal (HCI, MSKCC)
  • Read processing: FastQC, cutadapt
  • Alignment software: BWA, Bowtie, STAR, RSEM, Salmon
  • Alignment processing: Samtools, Picard
  • Variant detection: GATK, VarScan, MuTect, Strelka
  • Many more