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URL: http://cibiv.github.io/NextGenMap/
Proper Citation: NextGenMap (RRID:SCR_005488)
Description: A mapping program for Next Generation Sequencing reads 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.
Abbreviations: NGM
Synonyms: Nextgenmap - A mapping method for Next Generation Sequencing reads
Resource Type: software resource
Keywords: next-generation sequencing
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