CBI Software
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 CBI 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
- 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.
- MultiRepMacsChIPSeq, a multiple-replicate, multiple-sample pipeline for processing chromatin-based assays, including ChIP-Seq, ATAC-Seq, and Cut&Run. See our ChIPSeq page.
- S3Copy, a Java command-line utility for recursive downloading of files from AWS S3 buckets. This can automatically make Glacier restore requests and wait patiently until files are restored before downloading, making this a one-stop solution for retrieving archived GNomEx data from AWS accounts. See our Data Storage page.
Commercial Software
We have licenses for commercial software products:
- Novocraft novoalign alignment
Open-Source Software
This is a partial list of open-source software that we use and maintain on our compute infrastructure.