Hardware:

10 56-core 256G Haswell/Broadwell Nodes (Argon HPC cluster)

560 high-performance CPUs for running pipelines and software.  

Illumina Dragen-BioIT Platform On-Premise

One of the fastest and most accurate genomics data processing units in the world, based on a 48 core field-programmable gate array architecture (FPGAs).  

Pipelines:

The following is a current list of installed pipelines that we run internally (on Argon HPC) for projects: 

bcbio-nextgen 

A python toolkit providing best-practice pipelines for fully automated high throughput sequencing analysis. 

Nf-Core RNA-seq

Best-practices nextflow RNA-seq analysis pipeline from the open-source Nextflow Core community 

Nf-core smRNA-seq

Best-practices nextflow smRNA-seq analysis pipeline from the open-source Nextflow Core community 

10X Cellranger for scRNA-seq

Cell Ranger is a set of analysis pipelines that process Chromium single-cell data to align reads, generate feature-barcode matrices, perform clustering and other secondary analysis, and more. Cell Ranger includes four pipelines relevant to the 3' Single Cell Gene Expression Solution and related products.

10X Cellranger ARC 

The Single Cell Multiome ATAC + Gene Expression software suite consists of Cell Ranger ARC for the analysis and Loupe Browser for the visualization of chromatin accessibility and 3' gene expression data from the same cell produced by the 10x platform.

10X Spaceranger 

The Visium Spatial Gene Expression Software Suite is a set of software applications for analyzing and visualizing spatial gene expression data produced by the 10x Genomics Visium Platform. The software suite includes Space Ranger and Loupe Browser.

atac_NF

Custom nextflow-based pipeline to perform ATAC-seq analysis based on best-practice workflows. 

Illumina DRAGEN (Dynamic Read Analysis for GENomics)

The DRAGEN Platform is a combined hardware and software solution. It offers a variety of secondary analysis pipelines that are engineered to run on field-programmable gate array technology (FPGAs). FPGAs provide hardware-accelerated implementations of genomic analysis algorithms, including BCL conversion, mapping and alignment, sorting, duplicate marking, and haplotype variant calling.

Frameworks and commercial solutions: 

iPathwayGuide

iPathwayGuide enables IIHG Bioinformatics to analyze gene sets from RNA-Seq, ChIP-seq, ATAC-seq, microarrays, or other gene or protein expression experiments to identify the pathways, biological processes, networks, molecular functions, diseases, and cellular components that are implicated in a given phenotype.  In addition, iPathwayGuide provides sophisticated meta-analysis capabilities, as well as the ability to identify active microRNAs from mRNA data.  We create a cloud-based report from your gene set and share that report with you.  There is no software to install and no limit on the number of end-users or sharing of reports!  

Galaxy

The IIHG also has a local instance of Galaxy, a very friendly way to access high throughput bioinformatics tools through a web browser interface. If you have a hawkid, you can simply click here and set up an account. Please note, the Galaxy install is free to use and does not limit storage resources like the main instance of Galaxy. However, if you have more than 500Gb of storage for more than three months, we will begin to bill for storage according to our fee schedule.

GenomeTrax^®

The IIHG also has access to GenomeTrax^®, a highly-specialized database useful for annotating human variants. Due to licensing terms, it is only currently available to members of the Iowa Institute of Human Genetics. It is in the form of a Mysql database which is very useful for high throughput programmatic access but it does not have a friendly user interface. This software is primarily for advanced users.

Self-Serve Software

Ingenuity Pathway Analysis^®

Ingenuity Pathway Analysis^® (IPA).  IPA can be used for several applications, including transcriptomics, microRNA analysis, target discovery, drug repositioning, proteomics and metabolomics. To learn more about the University of Iowa's IPA license and how to get access click here.  

Partek Genome Studio^®

Partek Flow offers point and click analysis for next generation sequencing. To learn more about the University of Iowa's Partek Flow license and how to get access click here.