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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




No version available



  • person_outline Wan-Ping Lee

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

Publication for MOSAIK

MOSAIK citations


Genotyping of Plasmodiophora brassicae reveals the presence of distinct populations

BMC Genomics
PMCID: 5902848
PMID: 29661147
DOI: 10.1186/s12864-018-4658-1

[…] (assembly gca_000309985.1) and b. napus (assembly gca_000686985.1) genomes using deconseq 0.4.3 []. the demultiplexed reads were aligned to the p. brassicae genome (assembly gca_001049375.1) using mosaik 2.2.3 []. variant calling was performed using freebayes v0.9.21 []. the resulting vcf file was filtered by vcflib [] to retain variants present in 18 out of 21 […]


Novel read density distribution score shows possible aligner artefacts, when mapping a single chromosome

BMC Genomics
PMCID: 5836841
PMID: 29504893
DOI: 10.1186/s12864-018-4475-6

[…] []., we applied our benchmarking tests on 7 open source dna sequencing mapping tools, namely bowtie (1.1.1) [], bowtie2 (2.2.4) [], bwa (0.7.5 and 0.7.12 applying two algorithms) [], maq (0.7.1) [], mosaik (2.2.3) [], smalt (0.7.6) []. another 2 aligners have been rejected after repeated trials: bbmap (36.32) and gnumap (3.0.2). we also tried to compile blasr, gsnap and star, but without […]


Mitochondrial genome diversity and population structure of two western honey bee subspecies in the Republic of South Africa

Sci Rep
PMCID: 5778041
PMID: 29358597
DOI: 10.1038/s41598-018-19759-3

[…] bases with a phred score <20 (fastq_quality_filter -q 33 -q 20 -p 90) were removed. the resulting sequences were aligned to the bee mitochondria reference genome (ncbi accession nc_0015661) using mosaik aligner version 2.1.33 (parameters -mmp 0.05, -ls 500 -m all -a all)., illumina sequence reads were mapped to a.m. capensis and a.m. scutellata (kx870183 and kj601784.1) mitogenomes using […]


Accuracy of Programs for the Determination of Human Leukocyte Antigen Alleles from Next Generation Sequencing Data

Front Immunol
PMCID: 5733459
PMID: 29326702
DOI: 10.3389/fimmu.2017.01815

[…] for stem cell transplantation due to hematological malignancies. the sample from this study was not included in the study., improvements in the athlates results could be achieved by using the mosaik v2.2.3 () aligner as described in the athlates user manual 1.0 with the addition of the -om option to redirect multiple mapped reads to a separate bam file. when these reads were excluded […]


Genomic prediction accuracies in space and time for height and wood density of Douglas fir using exome capture as the genotyping platform

BMC Genomics
PMCID: 5712148
PMID: 29197325
DOI: 10.1186/s12864-017-4258-5

[…] out followed by a low quality filter that removed reads with more than 10% of the read with less than 20 quality score. the filtered reads were aligned against the reference transcriptome using mosaik v2.2.3 [] with the following parameters -mmp 0.05 -m all -a all -hs 15. snp markers were identified at a population level using freebayes [] without considering indels, multi-nucleotide […]


Functional dissection of Drosophila melanogaster SUUR protein influence on H3K27me3 profile

PMCID: 5709859
PMID: 29191233
DOI: 10.1186/s13072-017-0163-z

[…] protocol was used for library preparation, followed by sequencing on hiseq or miseq system (pair-end, 50 or 75 bp)., the reads obtained were mapped to bdgp r5/dm3 drosophila genome assembly using mosaik software [] with the following parameters: -m all -mmp 0.1 -act 20 -a single. for further analysis, only the reads that started with gatc sequence were retained. the number of reads […]

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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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