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Welcome to the DeepSeqAnalysis wiki!

This Github repo is the basis for the Deep Sequencing Analysis pages on ReadTheDocs, which are used as course material for a graduate class in applied bioinformatics at North Carolina State University. The term "applied bioinformatics" signifies that the emphasis of the class is not on algorithms, or how bioinformatics analyses work at the mathematical or computer science level. Instead, the target audience is life science students with little or no previous exposure to computational biology, and the goal is to empower the students to learn how to use new software and new analytical methods as they emerge. The enabling skills that are taught include command-line Linux utilities for file and directory management, how to read man pages and find information online, and basic scripting with bash and awk for format conversion, data management, and summarizing complex datasets. These skills are applied to examples of a variety of types of applied problems, including data QC and trimming of raw sequence reads, bacterial genome assembly, RNA-seq analysis for differential gene expression, ChIP-seq and other chromatin-structure-based analyses, and variant calling from reduced-representation or whole-genome sequencing, using open-source bioinformatics software in a virtual machine environment provided by NC State University resources. Time is available for comparison of open-source tools to commercial software packages, to evaluate the relative advantages of the ease of use of a graphic interface to the flexibility and power of the command-line.