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NextGenMap

A read mapper that is more than twice as fast as BWA, while achieving a mapping sensitivity similar to Stampy or Bowtie2. NextGenMap aligns reads reliably to a reference genome even when the sequence difference between target and reference genome is large, i.e. highly polymorphic genome. The software outperforms current mapping methods with respect to runtime and to the number of correctly mapped reads. NextGenMap handles automatically any read data independent of read length and sequencing technology. It may be used to map reads from nonstandard organism to a phylogenetically close reference genome or to apply it to metagenomics data.

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NextGenMap classification

NextGenMap specifications

Software type:
Package/Module
Restrictions to use:
None
Output format:
BAM, SAM
Parallelization:
CUDA
Version:
0.5.0
Maintained:
Yes
Interface:
Command line interface
Input format:
FASTA, FASTQ, SAM, BAM
Operating system:
Unix/Linux, Mac OS, Windows
Computer skills:
Advanced
Stability:
Stable

NextGenMap distribution

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NextGenMap support

Documentation

Credits

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Publications

Institution(s)

Center for Integrative Bioinformatics Vienna, Max F Perutz Laboratories, University of Vienna, Medical University of Vienna, Vienna, Austria; Bioinformatics and Computational Biology, Faculty of Computer Science, University of Vienna, Vienna, Austria

Funding source(s)

This work was supported by Deutsche Forschungsgemeinschaft SPP1174 [HA1628-9-2].

Link to literature

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