MOSAIK pipeline

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

 (16)
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 software49. 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: 5292751
PMID: 28165048
DOI: 10.1038/srep41960

[…] using mosaik alignment software49. 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 works with paired-end reads from illumina hiseq, and uses both a hashing scheme and the smith-waterman algorithm to produce gapped optimal alignments and to map exon junction-spanning reads […]

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 2.239–41. 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 […]

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 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, […]

2016
PMCID: 5154527
PMID: 27959952
DOI: 10.1371/journal.pone.0167989

[…] s.r.l. (udine, italy) using illumina 2 × 100 bp paired-end reads hiseq 2000 system. reads were trimmed, quality filtered, and mapped against h37rvsiena as a reference sequence (cp007027.1) using the mosaik assembler software [20]. genome fraction coverage and read depth were analyzed by qualimap software [21]., single nucleotide substitutions, insertions, and deletions were retrieved […]

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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