Identifying Highly Penetrant Disease Causal Mutations Using Next Generation Sequencing: Guide to Whole Process

Table 1

Tools for aligning reads to a reference genome.

Name	References	Comment
BFAST; Bowtie 2	[73]; [74]	These aligners use similar algorithms to determine contiguous sequences; however MAQ and BWA are widely used and have been praised for their computational efficiency and multiplatform compatibility [75].
BWA; MAQ; SOAP2	[76]; [77]; [78]

These are some of the many tools built for aligning reads produced from high throughput sequencing. Some have made speed their main purpose whereas others have paid more attention to annotating the files produced (such as mapping quality).