Tutorials¶

Domain-science QuickBytes: complete worked examples from genomics to materials science.

• Variant calling with GATK - A genomics variant-calling workflow using GATK best practices on CARC systems.
• Metabarcoding analysis - Process environmental DNA metabarcoding data on CARC clusters.
• RAD-seq analysis with Stacks - Analyze restriction-site associated DNA sequencing (RAD-seq) data with Stacks.
• Genome assembly evaluation with QUAST and BUSCO - Evaluate genome assembly quality and completeness with QUAST and BUSCO.
• Coalescent simulation with msprime - Simulate genealogical histories and genome sequences with msprime.
• Demographic inference with PSMC - Infer population size history from diploid genomes using PSMC.
• Bayesian phylogenetics with BEAST - Run BEAST Bayesian evolutionary analyses on CARC clusters.
• SimCov epidemiological simulation - Run the SimCov agent-based model of SARS-CoV-2 infection dynamics in lung tissue.
• VASP materials simulation - Set up and run VASP density-functional-theory calculations on CARC clusters.
• ORCA quantum chemistry - Run ORCA quantum chemistry calculations in parallel on CARC clusters.
• Parallel CASA for radio astronomy - Run mpiCASA for parallel radio astronomy imaging on CARC clusters.

Machine-readable versions of this page: Markdown twin · raw source on GitHub · llms.txt · llms-full.txt (whole site). See For AI agents.