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MOSAIK

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 forum

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MOSAIK classification

MOSAIK specifications

Software type:
Package/Module
Restrictions to use:
None
Operating system:
Unix/Linux
License:
GNU General Public License version 2.0, MIT License
Stability:
Stable
Interface:
Command line interface
Biological technology:
Illumina, Life Technologies, Pacific Biosciences, Roche
Programming languages:
C++
Computer skills:
Advanced
Maintained:
Yes

MOSAIK distribution

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MOSAIK support

Documentation

Maintainer

  • Wan-Ping Lee <>

Additional information

https://github.com/wanpinglee/MOSAIK/wiki MOSAIK is also incorporated into the command and pipeline launcher system gkno.

Credits

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Publications

Institution(s)

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.