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NextGenMap (NGM) is a flexible and fast read mapping program that is more than twice as fast as BWA, while achieving a mapping sensitivity similar to Stampy or Bowtie2. NextGenMap uses a memory efficient index structure (hash table) to store the positions of all 13-mers present in the reference genome. This index enables a quick identification of potential mapping regions for every read. Unlike other methods, NextGenMap dynamically determines for each read individually how many of the potential mapping regions have to be evaluated by a pairwise sequence alignment. Moreover, NextGenMap uses fast SIMD instructions (SSE) to accelerate the alignment calculations on the CPU. If available NextGenMap calculates the alignments on the GPU (using OpenCL/CUDA) resulting in a runtime reduction of another 20 - 50 %, depending on the underlying data set.

Installed version

The currently installed versions of NextGenMap is are

  • NextGenMap/0.5.2
  • NextGenMap/0.5.5-intel-2016b

on the environment hpc-uniol-env

Using NextGenMap on the HPC cluster

If you want to use NextGenMap on the HPC cluster, you can simply do that by loading its module with the command

module load NextGenMap

There is currently only one version of NextGenMap installed, thats why you dont have to specify a version. After the module is loaded, NextGenMap is usable. Use the command

ngm --help

to see the full syntax of the ngm-command and other useful informations.


The full documentation of NextGenMap can be found here.