MitoSeek protocols

View MitoSeek computational protocol

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MitoSeek specifications

Information


Unique identifier OMICS_05467
Name MitoSeek
Software type Pipeline/Workflow
Interface Command line interface
Restrictions to use None
Input data MitoSeek can extract mitochondrial genome information directly from a BAM file and also perform mitochondrial genome assembly.
Operating system Unix/Linux
Computer skills Advanced
Version 1.3
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Yan Guo <>

Publication for MitoSeek

MitoSeek in pipeline

2018
PMCID: 5827201
PMID: 29483551
DOI: 10.1038/s41598-018-21844-6

[…] ≥0.02 in allele fraction and the 99.999% confidence interval of the variant allele count under a binomial distribution did not overlap with the corresponding vaf in the normal. variants reported by mitoseek were further filtered for strand bias, in which variants were eliminated if they did not have ≥5 variant alleles called on each strand., in analyzing mutational processes in normal tissue, […]


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MitoSeek in publications

 (3)
PMCID: 5827201
PMID: 29483551
DOI: 10.1038/s41598-018-21844-6

[…] was originally generated at the canada’s michael smith genome sciences centre at the bc cancer agency using the illumina hiseq platform and aligned to the human hg18 reference sequence., the mitoseek tool was revised (supplementary methods) and used to extract mitochondrial dna reads from wgs bam files of 40 tumour-normal pairs, convert the mitochondrial genome coordinates from the hg18 […]

PMCID: 4889952
PMID: 27105841
DOI: 10.1093/nar/gkw309

[…] for whom conventional molecular testing had previously failed to produce a diagnosis. such evaluations of mtdna based on off-target data can be facilitated by dedicated bioinformatics tools such as mitoseek, which extracts mitochondrial genome information from exome data and analyses associated mutations and structural variants ()., based on the potency of this method for expanding knowledge […]

PMCID: 4872737
PMID: 26735174
DOI: 10.18632/oncotarget.6776

[…] switzerland) and the truseq sample preparation kit v2 (illumina, san diego, ca, usa)., whole exome sequencing data was filtered for mitochondrial sequences and screened for mt variants using the mitoseek tool [] and the revised cambridge reference sequence. thresholds were set to a coverage of > 50 reads per base. the mean coverage of mitochondrial variants was 212. an abundance […]


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MitoSeek institution(s)
Center for Quantitative Sciences, Vanderbilt University, Nashville, TN, USA; Center for Human Genetics Research, Vanderbilt University, Nashville, TN, USA

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