Glossary

Key Points

Background and Metadata	It’s important to record and understand your experiment’s metadata.
Assessing Read Quality	Quality encodings vary across sequencing platforms. FastQC and multiqc can generate quality control reports for sequencing data Keep your project directories tidy Files can be copied from HPC to your own machine for interactive visualisation
Trimming and Filtering	The options you set for the command-line tools you use are important! Data cleaning is an essential step in a genomics workflow.
Variant Calling Workflow	Bioinformatic command line tools are collections of commands that can be used to carry out bioinformatic analyses. To use most powerful bioinformatic tools, you’ll need to use the command line. There are many different file formats for storing genomics data. It’s important to understand what type of information is contained in each file, and how it was derived.
Automating a Variant Calling Workflow	We can combine multiple commands into a shell script to automate a workflow. Use `echo` statements within your scripts to get an automated progress update. We can give names to our output files and directories using variables
Running Genomics workflows on HPC	Job arrays can make our lives easier Some tools are able to use multiple threads
Workshop wrap-up	Many reproducible pipelines and workflows are already available No need to re-invent the wheel

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