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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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Versioning


No version available

Maintainer


  • person_outline David L. Robertson

Publication for Segminator

Segminator citations

 (11)
library_books

A Bioinformatic Pipeline for Monitoring of the Mutational Stability of Viral Drug Targets with Deep Sequencing Technology

2017
Viruses
PMCID: 5744132
PMID: 29168754
DOI: 10.3390/v9120357

[…] iral 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 and […]

library_books

Persistent HIV 1 replication maintains the tissue reservoir during therapy

2016
Nature
PMCID: 4865637
PMID: 26814962
DOI: 10.1038/nature16933

[…] e 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 er […]

library_books

Quantifying Next Generation Sequencing Sample Pre Processing Bias in HIV 1 Complete Genome Sequencing

2016
Viruses
PMCID: 4728572
PMID: 26751471
DOI: 10.3390/v8010012

[…] by 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 sequenc […]

library_books

Distinguishing low frequency mutations from RT PCR and sequence errors in viral deep sequencing data

2015
BMC Genomics
PMCID: 4425905
PMID: 25886445
DOI: 10.1186/s12864-015-1456-x

[…] ariants 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 b […]

library_books

Human APOBEC3 Induced Mutation of Human Immunodeficiency Virus Type 1 Contributes to Adaptation and Evolution in Natural Infection

2014
PLoS Pathog
PMCID: 4117599
PMID: 25080100
DOI: 10.1371/journal.ppat.1004281

[…] ell 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 as a r […]

library_books

Ultra deep mutant spectrum profiling: improving sequencing accuracy using overlapping read pairs

2013
BMC Genomics
PMCID: 3599684
PMID: 23402258
DOI: 10.1186/1471-2164-14-96

[…] ished studies have begun to target more of the genome with high depths using the greater sequencing output of Illumina technologies [,]. Recently, the software tool for managing deep sequencing data, Segminator II, was introduced and used to compare performance of Illumina and 454 deep sequencing of influenza []. However, less emphasis was given to evaluating a general subconsensus base calling pr […]

Citations

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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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