Background and Metadata
- It is important to record and understand your experiment’s metadata.
Assessing Read Quality
- Quality encodings vary across sequencing platforms.
-
for
loops let you perform the same set of operations on multiple files with a single command.
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 will need to use the command line.
- There are many different file formats for storing genomics data. It is 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.