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seqsphere+ bionumerics clc genomics workbench  (Ridom GmbH)

 
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    Structured Review

    Ridom GmbH seqsphere+ bionumerics clc genomics workbench
    Seqsphere+ Bionumerics Clc Genomics Workbench, supplied by Ridom GmbH, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/computer+software+package%2C+bionumeric/seqsphere/pmc08743536-34-3-1
    Average 90 stars, based on 1 article reviews
    seqsphere+ bionumerics clc genomics workbench - by Bioz Stars, 2026-09
    90/100 stars

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    Related Articles

    Construct:

    Article Title: Comparative genomic analysis of resistance and virulence genes in staphylococcus epidermidis and their impact on clinical outcome of musculoskeletal infections.
    Article Snippet: Genome processing was performed on the BV-BRC platform (https://www.bvbrc.org/) with Ridom SeqSphere + v9.0 software (Münster, Germany).

    Article Title: Genomic Epidemiology of Enterococcus faecium Bloodstream Infections During a VanB-type VRE Peak Reveals an Oligoclonal Scenario: An Observational Study at a German University Hospital (2017–2022)
    Article Snippet: MLST and cgMLST were carried out using established typing schemes in Ridom SeqSphere+ v9.0.10 ( , ).

    Article Title: Staphylococcus aureus From Prosthetic Joint Infections and Blood Cultures Display the Same Genetic Background.
    Article Snippet: Sequences were trimmed to an average Phred quality score of 30 in 20 bp windows, assembled using optimized k- mer size, downsampled to 120× using version 1.1.04 of Velvet, and assigned multilocus sequence type (ST), clonal complex (CC), and core genome multilocus sequence typing (cgMLST) complex type [13] using version 7.2.0 of SeqSphere+ (Ridom GmbH, Münster, Germany).

    Article Title: Multi-host distribution of Rhodococcus equi (Prescottella equi) strains and their phylogenomic clustering
    Article Snippet: Tree constructed using ad hoc core-genome MLST (cgMLST) scheme containing 2’737 genes generated in Ridom Seqsphere + v9.0.1 ( https://www.ridom.de/seqsphere/cgmlst/ ) and converted to a neighbor-joining phylogeny using the R package ape [ ].

    Article Title: Interpreting whole-genome sequencing data during neonatal Klebsiella oxytoca complex outbreak management.
    Article Snippet: The resulting genome sequences were analysed using Ridom SeqSphere (v8 4.1).

    Article Title: High genetic relatedness between multidrug resistant bacteria before and after the 2022 invasion of Ukraine.
    Article Snippet: First, core genome MLST was performed in SeqSphere + Software v 7.7.2 (Ridom, Germany) using the cgMLST schemes developed for P. aeruginosa [36] and A. baumannii [37] with a cutoff of 90%.

    Article Title: Multi-host distribution of Rhodococcus equi (Prescottella equi) strains and their phylogenomic clustering
    Article Snippet: Core-genome MLST (cgMLST) analysis for 286 R. equi genomes was performed in Ridom Seqsphere+ (v9.0.1; Ridom GmbH, Münster, Germany).

    Generated:

    Article Title: Comparative genomic analysis of resistance and virulence genes in staphylococcus epidermidis and their impact on clinical outcome of musculoskeletal infections.
    Article Snippet: Genome processing was performed on the BV-BRC platform (https://www.bvbrc.org/) with Ridom SeqSphere + v9.0 software (Münster, Germany).

    Article Title: Genomic Epidemiology of Enterococcus faecium Bloodstream Infections During a VanB-type VRE Peak Reveals an Oligoclonal Scenario: An Observational Study at a German University Hospital (2017–2022)
    Article Snippet: MLST and cgMLST were carried out using established typing schemes in Ridom SeqSphere+ v9.0.10 ( , ).

    Article Title: Staphylococcus aureus From Prosthetic Joint Infections and Blood Cultures Display the Same Genetic Background.
    Article Snippet: Sequences were trimmed to an average Phred quality score of 30 in 20 bp windows, assembled using optimized k- mer size, downsampled to 120× using version 1.1.04 of Velvet, and assigned multilocus sequence type (ST), clonal complex (CC), and core genome multilocus sequence typing (cgMLST) complex type [13] using version 7.2.0 of SeqSphere+ (Ridom GmbH, Münster, Germany).

    Article Title: Multi-host distribution of Rhodococcus equi (Prescottella equi) strains and their phylogenomic clustering
    Article Snippet: Tree constructed using ad hoc core-genome MLST (cgMLST) scheme containing 2’737 genes generated in Ridom Seqsphere + v9.0.1 ( https://www.ridom.de/seqsphere/cgmlst/ ) and converted to a neighbor-joining phylogeny using the R package ape [ ].

    Article Title: Interpreting whole-genome sequencing data during neonatal Klebsiella oxytoca complex outbreak management.
    Article Snippet: The resulting genome sequences were analysed using Ridom SeqSphere (v8 4.1).

    Article Title: High genetic relatedness between multidrug resistant bacteria before and after the 2022 invasion of Ukraine.
    Article Snippet: First, core genome MLST was performed in SeqSphere + Software v 7.7.2 (Ridom, Germany) using the cgMLST schemes developed for P. aeruginosa [36] and A. baumannii [37] with a cutoff of 90%.

    Article Title: Multi-host distribution of Rhodococcus equi (Prescottella equi) strains and their phylogenomic clustering
    Article Snippet: Core-genome MLST (cgMLST) analysis for 286 R. equi genomes was performed in Ridom Seqsphere+ (v9.0.1; Ridom GmbH, Münster, Germany).

    Isolation:

    Article Title: Comparative genomic analysis of resistance and virulence genes in staphylococcus epidermidis and their impact on clinical outcome of musculoskeletal infections.
    Article Snippet: Genome processing was performed on the BV-BRC platform (https://www.bvbrc.org/) with Ridom SeqSphere + v9.0 software (Münster, Germany).

    Article Title: Genomic Epidemiology of Enterococcus faecium Bloodstream Infections During a VanB-type VRE Peak Reveals an Oligoclonal Scenario: An Observational Study at a German University Hospital (2017–2022)
    Article Snippet: MLST and cgMLST were carried out using established typing schemes in Ridom SeqSphere+ v9.0.10 ( , ).

    Article Title: Staphylococcus aureus From Prosthetic Joint Infections and Blood Cultures Display the Same Genetic Background.
    Article Snippet: Sequences were trimmed to an average Phred quality score of 30 in 20 bp windows, assembled using optimized k- mer size, downsampled to 120× using version 1.1.04 of Velvet, and assigned multilocus sequence type (ST), clonal complex (CC), and core genome multilocus sequence typing (cgMLST) complex type [13] using version 7.2.0 of SeqSphere+ (Ridom GmbH, Münster, Germany).

    Article Title: Multi-host distribution of Rhodococcus equi (Prescottella equi) strains and their phylogenomic clustering
    Article Snippet: Tree constructed using ad hoc core-genome MLST (cgMLST) scheme containing 2’737 genes generated in Ridom Seqsphere + v9.0.1 ( https://www.ridom.de/seqsphere/cgmlst/ ) and converted to a neighbor-joining phylogeny using the R package ape [ ].

    Article Title: Interpreting whole-genome sequencing data during neonatal Klebsiella oxytoca complex outbreak management.
    Article Snippet: The resulting genome sequences were analysed using Ridom SeqSphere (v8 4.1).

    Article Title: High genetic relatedness between multidrug resistant bacteria before and after the 2022 invasion of Ukraine.
    Article Snippet: First, core genome MLST was performed in SeqSphere + Software v 7.7.2 (Ridom, Germany) using the cgMLST schemes developed for P. aeruginosa [36] and A. baumannii [37] with a cutoff of 90%.

    Article Title: Multi-host distribution of Rhodococcus equi (Prescottella equi) strains and their phylogenomic clustering
    Article Snippet: Core-genome MLST (cgMLST) analysis for 286 R. equi genomes was performed in Ridom Seqsphere+ (v9.0.1; Ridom GmbH, Münster, Germany).

    Plasmid Preparation:

    Article Title: Comparative genomic analysis of resistance and virulence genes in staphylococcus epidermidis and their impact on clinical outcome of musculoskeletal infections.
    Article Snippet: Genome processing was performed on the BV-BRC platform (https://www.bvbrc.org/) with Ridom SeqSphere + v9.0 software (Münster, Germany).

    Article Title: Genomic Epidemiology of Enterococcus faecium Bloodstream Infections During a VanB-type VRE Peak Reveals an Oligoclonal Scenario: An Observational Study at a German University Hospital (2017–2022)
    Article Snippet: MLST and cgMLST were carried out using established typing schemes in Ridom SeqSphere+ v9.0.10 ( , ).

    Article Title: Staphylococcus aureus From Prosthetic Joint Infections and Blood Cultures Display the Same Genetic Background.
    Article Snippet: Sequences were trimmed to an average Phred quality score of 30 in 20 bp windows, assembled using optimized k- mer size, downsampled to 120× using version 1.1.04 of Velvet, and assigned multilocus sequence type (ST), clonal complex (CC), and core genome multilocus sequence typing (cgMLST) complex type [13] using version 7.2.0 of SeqSphere+ (Ridom GmbH, Münster, Germany).

    Article Title: Multi-host distribution of Rhodococcus equi (Prescottella equi) strains and their phylogenomic clustering
    Article Snippet: Tree constructed using ad hoc core-genome MLST (cgMLST) scheme containing 2’737 genes generated in Ridom Seqsphere + v9.0.1 ( https://www.ridom.de/seqsphere/cgmlst/ ) and converted to a neighbor-joining phylogeny using the R package ape [ ].

    Article Title: Interpreting whole-genome sequencing data during neonatal Klebsiella oxytoca complex outbreak management.
    Article Snippet: The resulting genome sequences were analysed using Ridom SeqSphere (v8 4.1).

    Article Title: High genetic relatedness between multidrug resistant bacteria before and after the 2022 invasion of Ukraine.
    Article Snippet: First, core genome MLST was performed in SeqSphere + Software v 7.7.2 (Ridom, Germany) using the cgMLST schemes developed for P. aeruginosa [36] and A. baumannii [37] with a cutoff of 90%.

    Article Title: Multi-host distribution of Rhodococcus equi (Prescottella equi) strains and their phylogenomic clustering
    Article Snippet: Core-genome MLST (cgMLST) analysis for 286 R. equi genomes was performed in Ridom Seqsphere+ (v9.0.1; Ridom GmbH, Münster, Germany).



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