MOSAIK specifications


Unique identifier OMICS_00669
Software type Package/Module
Interface Command line interface
Restrictions to use None
Biological technology Illumina, Life Technologies, Pacific Biosciences, Roche
Operating system Unix/Linux
Programming languages C++
License GNU General Public License version 2.0, MIT License
Computer skills Advanced
Stability Stable
Maintained Yes



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  • person_outline Wan-Ping Lee <>

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

MOSAIK article

MOSAIK citations

PMCID: 5013636

[…] specificity., rna sequencing (illumina hi-seq) yielded 30–40 million read pairs for each sample. the mrna-seq paired-end reads were aligned to the human reference genome, grch37/hg19, using the mosaik alignment software73. the mrna-seq mouse sample reads were aligned onto the mouse genome build ucsc mm10 (ncbi 38). the overlaps between aligned reads and annotated genomic features, […]

PMCID: 4525489

[…] the dynamic trimming approach implemented in solexqa (cox et al., 2010), using a phred score of 30 as the base call quality threshold. trimmed reads were then mapped on the reference genome using mosaik aligner with default parameters (lee et al., 2014). only those snps that (i) were not present in the wt strain, (ii) were supported by, at least, eight reads, and (iii) had a support greater […]

PMCID: 4046713

[…] illumina rta software version 1.13.48., sequence reads were trimmed to remove illumina adapter sequences with cutadapt version 1.1 [34] and aligned to the human reference genome (version hg19) with mosaik version 2.1.33 with default parameters. realignment and recalibration of base quality scores using dbsnp137 was performed with gatk version 1.0.5909 [31]. read realignment was performed around […]

PMCID: 3526165

[…] for 4 s. empcr and bidirectional sequencing were performed according to the manufacturer's instructions (roche 454)., base calling and alignment were performed using the algorithm of pyrobayes and mosaik. subsequent analysis of variants was performed using the custom r library flowgram. to maximize specificity for very low-level variants, base positions within or immediately adjacent […]

PMCID: 3125267

[…] flowgram data was processed using a custom analysis pipeline. briefly, data were trimmed by sequence quality and aligned against a reference database of all known macaque kir sequences using the mosaik aligner ( the reference library of kir sequences was obtained from the immuno polymorphism database [29]. polymorphisms between reads […]

MOSAIK institution(s)
Department of Biology, Boston College, Chestnut Hill, MA, USA; Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA, USA
MOSAIK funding source(s)
Supported by NIH: 5R01HG004719-04 and NIH: 3U01HG006513-02S1.

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