4. Alignment overview

Alignment is the process of taking the 100bp reads from the FASTQ and places them in the correct location in the genome. However, there exist a variety of aligners that will accomplish this goal -- this tutorial will help you consider the pros and cons of each aligner.

Some background on aligners:

All aligners require the reference sequence to be indexed -- this is a process that creates additional files that describe the reference file, such as where each chromosome is located in the file. Knowing this information speeds up alignment. Each aligner indexes in a particular way. How to index will be covered in each aligner's section.

All of the aligners are capable of taking advantage of multi-threading: splitting up the work of alignment across multiple cores. Your instance has 16 available cores, so you will instruct the aligner to split up the alignment into 16 pieces.

You are now ready to start indexing your references!