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Table of Contents

Table of Contents
excludeTable of Contents

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.


two of the most versatile mappers: BWA and Bowtie2, the latter being part of the Tuxedo suite (e.g. Tophat2).

Theoretical Background and Possible Cases


Reference Genomes


BWA - The Most General Mapper

 Bowtie and

Bowtie2 - More


Pain, More




Future Directions


Table of Contents