The GMA suite is used for measuring how well NGS reads can be mapped to reference genomes, especially for discovering variations
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Bioinformatics. 2012 Aug 15;28(16):2097-105. doi: 10.1093/bioinformatics/bts330. Epub 2012 Jun 4.
Genomic dark matter: the reliability of short read mapping illustrated by the genome mappability score.
Lee H1, Schatz MC.