Segminator statistics

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Associated diseases

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Segminator specifications

Information


Unique identifier OMICS_12135
Name Segminator
Software type Pipeline/Workflow
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages Java
Computer skills Advanced
Version 2.0
Stability Alpha
Maintained Yes

Taxon


  • Primates
    • Homo sapiens
  • Viruses
    • Human immunodeficiency virus 1
    • Human immunodeficiency virus 2

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Maintainer


  • person_outline David L. Robertson <>

Publication for Segminator

Segminator in publications

 (9)
PMCID: 5744132
PMID: 29168754
DOI: 10.3390/v9120357

[…] drug targets. they also do not include the options to generate the output data in terms of statistically significant mutation profiles and to refine the target under mutations automatically. the segminator ii package developed by archer et al. [] is the closest in terms of the aims and abilities of the pipeline presented in this paper. however, this package has not been updated since 2012 […]

PMCID: 4865637
PMID: 26814962
DOI: 10.1038/nature16933

[…] temporally and spatially linked deep-sequencing data for studying viral diversity, the viral sequences were first aligned against the hxb2 reference sequence (genbank accession number k03455) using segminator ii (version 0.1.1). we then generated a consensus viral sequence for each patient as a reference for assembly to improve the alignment quality. a statistical model that utilizes platform […]

PMCID: 4728572
PMID: 26751471
DOI: 10.3390/v8010012

[…] the 454 software. prior to the read cleaning with rc454 [], reads with an exact match to both the barcode and, for the nextera™-fragmented samples, the transposon end sequences were extracted with segminator ii [] and assigned to the corresponding sample. when available, we used patient-specific reference sequences obtained by sanger sequencing to map the reads (see ). de novo assembled […]

PMCID: 4425905
PMID: 25886445
DOI: 10.1186/s12864-015-1456-x

[…] from erroneous mutations, with the majority of methods tailored to the 454 platform such as ampliconnoise [] and readclean454 []. other tools aimed at detecting low frequency variants include segminator ii [] which is specialised towards temporally sampled data, v-phaser which utilises information on the co-location of variants on reads [,], lo-freq which utilises quality scores to model […]

PMCID: 4117599
PMID: 25080100
DOI: 10.1371/journal.ppat.1004281

[…] culture experiments, taking into account data-specific indels, and thereby reducing dependency on a generic template., we aligned the viral sequences obtained from peripheral blood from patients by segminator ii (version 0.1.1) using the hxb2 sequence (genbank accession number k03455) as a reference for assembly , , . we generated a consensus sequence for each patient, which was then used […]


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Segminator institution(s)
Faculty of Life Sciences, University of Manchester, Manchester, UK; Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK; Life Sciences, Branford, CT, USA; British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada; Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada; Pfizer Global Research and Development, Sandwich, UK
Segminator funding source(s)
Supported by Pfizer Global R&D; the BBSRC (grant BB/ H012419/1) and the Apple Research & Technology Support programme.

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