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Welcome to the UConn CBC wiki!

This site serves to organize some of the documentation we create for users of the UConn Computational Biology Core and the Xanadu computer cluster. You can also access this documentation through our website.

HPC and SLURM Resources

The Xanadu Cluster

• Introduction to the Xanadu Cluster - Video Series
• Understanding the Xanadu Cluster
• So you want to use a GPU on Xanadu...

The Mantis Cluster

• Welcome to Mantis Cluster

General HPC/Slurm guidance for UCHC clusters

• Requesting resource allocations in SLURM
• Using job arrays in SLURM
• Monitoring cluster usage
• Random HPC and Bioinformatics Tips

Software

• [ The module system ]
• [ Software containers ]
• [ Compiling your own software ]

Connecting development environments to Xanadu

• Visual Studio Code
• RStudio
• Jupyter notebooks

Data Management and Transfer:

• Data Storage and Guidelines
• Transfer Files
• Data Download from Basespace

Databases

• [ Databases ]

Commercial Software:

• Geneious
• IPA

CBC Data analysis tutorials

• Genome assembly
• Genome annotation
• Variant Calling
• RADseq
• RNA-seq (Non-model)
• RNA-seq with reference genome and annotation
• [ Genome Size Estimation (Estimate genome size with k-mer based analysis of short read data (Jellyfish/R/GenomeScope)

Basic Bioinformatics Stuff

• Unix Basics
• [ Unix Examples ]
• [ Vim Editor ]
• [ Introduction to R ]