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nextgenmap website  

NextGenMap is a flexible highly sensitive short read mapping tool that handles much higher mismatch rates than comparable algorithms while still outperforming them in terms of runtime. This allows analyzing large-scale datasets even with increased SNP rates or higher error rates (e.g. caused by specialized experimental protocols) and avoids bias…

Environment Modules

Run module spider nextgenmap to find out what environment modules are available for this application.

System Variables

  • HPC_NEXTGENMAP_DIR - installation directory
  • HPC_NEXTGENMAP_BIN - executable directory


If you publish research that uses nextgenmap you have to cite it as follows:

NextGenMap: fast and accurate read mapping in highly polymorphic genomes. Bioinformatics (2013) 29 (21): 2790-2791 first published online August 23, 2013 doi:10.1093/bioinformatics/btt468