MOSAIK protocols

View MOSAIK computational protocol

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MOSAIK specifications

Information


Unique identifier OMICS_00669
Name MOSAIK
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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Documentation


Maintainer


  • person_outline Wan-Ping Lee <>

Additional information


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

Publication for MOSAIK

MOSAIK in pipelines

 (21)
2017
PMCID: 5292751
PMID: 28165048
DOI: 10.1038/srep41960

[…] of herv-k108, k109, k113, and k115 were downloaded from ncbi genbank. mapping/alignment: the raw paired-end reads in fastq format were aligned to the human reference genome, grch37/hg19, using mosaik alignment software. the raw paired-end reads in fastq format were also aligned to the human endogenous virus herv-k108, k109, k113, and k115 reference genome sequences, respectively. mosaik […]

2017
PMCID: 5679167
PMID: 28983013
DOI: 10.1084/jem.20162123

[…] reference sequence) using iterative virus assembler ()., gaps in the de novo assembled genomes were filled using maternal or a reference sequence. the reads were then mapped to the assemblies using mosaik () with default parameters. a subtype c reference genome was annotated with the location of the epitopes of interest. the de novo assemblies were aligned using muscle () to the annotated […]

2017
PMCID: 5681693
PMID: 29127275
DOI: 10.1038/s41467-017-01631-z

[…] management of scientific data. briefly, raw reads were trimmed by sequence quality using trimmomatic and aligned against a reference library comprised of published mhc sequences using the aligner mosaik, version 2.2–. perfect matches between reads and reference alleles were scored using custom software that utilized hts-jdk (http://samtools.github.io/htsjdk/)., the initial flu-bu-tbi reduced […]

2016
PMCID: 5013636
PMID: 27574101
DOI: 10.1038/ncomms12601

[…] 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 software. 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, […]

2016
PMCID: 5210029
PMID: 28058113
DOI: 10.1093/ve/vew033

[…] de novo assembled using trinity () to build the consensus powv genome, which was deposited in genbank (accession number ku886216). all samples were then aligned to the powv consensus sequence using mosaik () and duplicate reads were removed using the markduplicates tool within picard to limit the influence of pcr artifacts. isnvs and ilvs (includes both single and double insertions […]


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MOSAIK in publications

 (183)
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 [https://github.com/ekg/vcflib] to retain variants present in 18 out of 21 […]

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 […]

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 […]

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 […]

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 […]


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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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