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Maps next generation sequencing (NGS) reads to a reference genome. MOSAIK is a reference-guided aligner that uses a neural-network based training scheme and supports most existing sequencing technologies. The software uses a Smith-Waterman algorithm and can align reads to a genome using the International Union of Pure and Applied Chemistry (IUPAC) ambiguity codes, ensuring that alignments against known single nucleotide polymorphisms (SNPs) are not penalized. It additionally provides explicit support for structural variant (SV) detections.

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MOSAIK classification

MOSAIK specifications

Software type:
Restrictions to use:
Operating system:
GNU General Public License version 2.0, MIT License
Command line interface
Biological technology:
Illumina, Life Technologies, Pacific Biosciences, Roche
Programming languages:
Computer skills:

MOSAIK distribution


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MOSAIK support



  • Wan-Ping Lee <>

Additional information MOSAIK is also incorporated into the command and pipeline launcher system gkno.


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Department of Biology, Boston College, Chestnut Hill, MA, USA; Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA, USA

Funding source(s)

Supported by NIH: 5R01HG004719-04 and NIH: 3U01HG006513-02S1.

Link to literature

By using OMICtools you acknowledge that you have read and accepted the terms of the end user license agreement.