Mobster protocols

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Mobster specifications

Information


Unique identifier OMICS_09836
Name Mobster
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data Sequence data
Input format BAM
Operating system Unix/Linux
Programming languages Java
License GNU General Public License version 2.0
Computer skills Advanced
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Djie Tjwan Thung <>

Publication for Mobster

Mobster in pipeline

2015
PMCID: 4785551
PMID: 27081539
DOI: 10.1038/hgv.2015.30

[…] end modules. the sequencing data were mapped to a human genome reference (hg19) using a standard method of bwa, picard, and gatk, as previously described., mei detection was conducted using mobster with the default setting. to manually review meis, meis with split read(s) were maintained. mobster detected a total of 106 (29 l1 and 77 alu) meis with split reads from the 44 ovarian cancer […]


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Mobster in publications

 (4)
PMCID: 5737362
PMID: 28985298
DOI: 10.1093/gbe/evx170

[…] 146,268 gaps totaling to 38 mega base pairs (mb) in the polar bear genome; the majority of these gaps (138,041) were >1 bp., reference mapped short reads were processed with retroseq () and mobster () to identify insertions that are present in the corresponding genome while being absent in the reference genome. for retroseq, a minimum mapping quality of 30 and a te mapping identity […]

PMCID: 5305044
PMID: 28228978
DOI: 10.1080/2159256X.2017.1280116

[…] refinement of next-generation sequence based te insertion calling methods resulting in the tangram and melt programs, for the second and third phases of the project, respectively. retroseq and mobster are two of the other most widely used programs for sequence based te insertion detection. retroseq was implemented primarily for the detection of endogenous retrovirus insertions in the mouse […]

PMCID: 4785551
PMID: 27081539
DOI: 10.1038/hgv.2015.30

[…] cause diseases such as cancer. we conducted mobile element insertion (mei) profiling of 44 epithelial ovarian cancers using exome-sequencing data. we identified a total of 106 meis using the mobster program, 8 of which were novel exonic meis., mobile elements are major components of the human genome, comprising between 45 and 66% of the genome. mobile elements have contributed […]

PMCID: 4479793
PMID: 26161383
DOI: 10.3389/fbioe.2015.00092

[…] mosaik (lee et al., ) alignments (though it may use alignments produced by other mappers), next-generation variationhunter (hormozdiari et al., ), tea (lee et al., ), retroseq ekeane:2013kq, and mobster (thung et al., ) have been reported in the literature., overall, all the approaches discussed are fairly limited with respect to repeated regions of the reference genome (alkan et al., , ). […]


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Mobster institution(s)
Department of Human Genetics, RadboudUMC, Nijmegen, HB, Netherlands

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