Overview and Objectives
Once raw sequence files are generated (in FASTQ format) and quality-checked, the next step in most NGS pipelines is mapping to a reference genome. For individual sequences of interest, it is common to use a tool like BLAST to identify genes or species of origin. However, a typical example will have millions of reads, and a reference space that is frequently billions of bases, which BLAST and similar tools are not really designed to handle.
Thus, a large set of computational tools have been developed to quickly, and with sufficient (but NOT absolute) accuracy align each read to its best location, if any, in a reference. Even though many mapping tools exist, a few individual programs have a dominant "market share" of the NGS world. These programs vary widely in their design, input, output, and applicability. In this section, we will primarily focus on three mappers that are all widely useful for many NGS situations: BWA, Bowtie, and Bowtie2.
Theoretical Background and Possible Cases
BWA - The Most General Mapper
Bowtie and Bowtie2 - More Gain, More Pain