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NGS Data http://en.wikibooks.org/wiki/Next_Generation_Sequencing_(NGS). BWA http://bioinformatics.oxfordjournals.org/content/25/14/1754.full. Bowtie.
NGS Data

http://en.wikibooks.org/wiki/Next_Generation_Sequencing_(NGS)

BWA

http://bioinformatics.oxfordjournals.org/content/25/14/1754.full

Bowtie

http://genomebiology.com/2009/10/3/R25

GATK

http://www.nature.com/ng/journal/v43/n5/full/ng.806.html

BWA and Bowtie are the most popular alignment tools in mapping the short reads of the NGS data to a reference genome. If a reference genome exists for the organism, then it is enough to map the short read to the reference Due to high sequence similarity within members of the same species. GATK is a framework, used by many researchers to detect the variation in the sequenced DNA.