Pre-loaded software in the UKB-RAP

About the Tools Library

The Research Analysis Platform provides a full-featured toolkit for preparing and analysing a wide range of datatypes. The Tools Library under the Tools tab of the platform shows a complete list of apps and workflows available to you. Use filters to quickly find items by name, category, etc.

Learning about Individual Apps

Clicking on the name of an app will open up a separate information page which contains details about the app's inputs, outputs, and other documentation details. For apps encapsulating existing bioinformatics tools this page also contains licensing information, links to the website for that software, and citations to any related publications. This page also shows the version history for the app and developer documentation which describes the inner workings of the app in detail.

Genomics Apps

1. Swiss Army Knife app provides access to the following tools: 
   • BCFtools
   • BEDtools
   • VCFtools
   • vcflib
   • PLINK
   • PLINK2
   • Sambamba
   • SAMtools
   • Picard
   • Tabix
   • Seqtk
   • bgzip
   • bgenix
2. FastQC
3. Qualimap2
4. BWA-MEM
5. GATK4 apps
   • Germline Best Practice BAM/CRAM to VCF workflow
   • Base Quality Score recalibrator 
   • HaplotyleCaller
   • Single-Sample GenotypeGVCFs genotyper
6. CNVkit
7. SnpEff
8. SnpSift
9. Multi-QC
10. GLnexus
11. OQFE
12. Parabricks DeepVariant
13. DRAGEN 3.7.8 UKB WGS Germline 

Translational Analysis Apps

1. Swiss Army Knife app provides access to the following tools: 
   • PLINK
   • PLINK2
   • PLATO
   • BOLT-LMM
   • REGENIE
   • QCTool
2. SAIGE apps
   • Genetic relatedness matrix (GRM) generator 
   • Sparse GRM generator 
   • Single variant association tester
   • Gene and region based association tester 
3. PHESANT
4.  PLINK2 GWAS
5. RAREMETAL2
6. PRSice-2
7. EIGENSOFT
8. LocusZoom
9. JupyterLab app with PYTHON_R and JupyterLab with Spark Cluster apps provide access to the following R packages:
   • BiocManager
   • MendelianRandomization
   • coloc
   • HyPrColoc
   • epiR
   • prevalence 
   • incidence
   • outbreak
10. JupyterLab with Spark Cluster app provides access to:
    • Hail
    • VEP

Statistical Analysis

1. JupyterLab app and JupyterLab with Spark Cluster app provide access to:
   • NumPy
   • SciPy
   • Matplotlib
   • Seaborn
   • Pandas
2. JupyterLab app with STATA feature provides access to:
   • Stata (stata license to be provided by the user)

Image Processing 

1. JupyterLab app with IMAGE_PROCESSING feature provides access to:
   1. nipype
   2. FreeSurfer
   3. FSL

ML frameworks

1. JupyterLab app with ML feature provides access to:
   • tensorflow
   • torch
   • cntk
   • keras
   • scikit-Learn
2. JupyterLab with Spark Cluster app provides access to:
   • MLlib 

Utility Apps

1. URL Fetcher fetches and uploads a file from a remote URL to the platform
2. AWS S3 Importer transfers files from S3 bucket to the platform
3. ttyd provides a web-based terminal to a platform virtual machine
4. Cloud Workstation provides an shh-accessible workstation
5. Table exporter exports a specific entity or the cohort table to CSV 
6. Dataset Extender ingests a data file and create a new, superset Dataset
7. Rebase Cohorts and Dashboards move cohorts from one Dataset to another in your application