Genomic Data Analysis: NGS data wrangling on the command line: Glossary

Quality encodings vary across sequencing platforms.

for loops let you perform the same set of operations on multiple files with a single command.

The options you set for the command-line tools you use are important!

Data cleaning is an essential step in a genomics workflow.

Bioinformatics command line tools are collections of commands that can be used to carry out bioinformatics analyses.

To use most powerful bioinformatics 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.

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.