Modern genomics starts with next-generation sequencing (NGS), which reads millions of short DNA fragments at once. The raw output is a large set of reads, and not all of them are good. Before any analysis, you need to check the data and clean it up.
You'll start with how Illumina sequencing by synthesis works, so you know where the reads and their quality scores come from. Then you'll learn to run FastQC, read its report, and spot problems such as low-quality bases or leftover adapter sequence.
Finally, you'll fix those problems with Trimmomatic, which trims low-quality bases and adapters and can handle paired-end reads. You then run FastQC again to confirm the data improved. This check-trim-recheck routine is the first step of almost every sequencing project. Once you've finished, move on to Genomics & Variant Calling.
A 3D look at the Illumina workflow, from sample preparation and cluster generation to sequencing by synthesis and data analysis.
How to read the FastQC report, a tool for assessing the quality of NGS data. This part covers the remaining sections of the report.
How to assess raw data quality with FastQC, trim it with Trimmomatic, filter it, and then check the quality again.
Trimming and quality control of raw FASTQ reads, including paired-end data.