Journal: Clinical Microbiology Reviews

Article Title: A Primer on Infectious Disease Bacterial Genomics

doi: 10.1128/CMR.00001-16

Figure Lengend Snippet: List of bioinformatics analysis resources

Article Snippet: For those lacking resources or time for a local HTS data analysis environment, SaaS may be the preferred option so long as requisite analysis software is available to achieve project goals. table ft1 table-wrap mode="anchored" t5 TABLE 3 caption a7 Type Name Cost Comments Cloud services (IaaS/PaaS) Amazon Web Services (Amazon.com Inc., Seattle, WA, USA) Commercial Commercial cloud environments providing resources to construct customized high-performance computing environments; acts as a base from which additional software (e.g., Galaxy) can be utilized Microsoft Azure (Microsoft, Redmond, WA, USA) Commercial Google Cloud Platform (Google, Mountain View, CA, USA) Commercial Cloud services (SaaS) Illumina BaseSpace (San Diego, CA, USA) Commercial Commercial cloud-based bioinformatics analysis environments associated with different sequencing instruments; provides analysis tools and data management fine-tuned for each sequencing instrument; often integrates free and open-source bioinformatics tools described in this review (e.g., FastQC for quality control of sequence reads) Thermo Fisher Cloud (South San Francisco, CA, USA) Commercial Metrichor (Oxford, UK) Commercial DNAnexus (Mountain View, CA, USA) Commercial Cloud-based bioinformatics environment not specifically tied to any sequencing platform Web services Galaxy ( 24 ) Free Free and open-source bioinformatics analysis environment available at https://galaxyproject.org/ ; private instances can be installed on local hardware or within a cloud-based environment; RAST ( 29 ) Free Web service focused on genome annotation; available at http://rast.nmpdr.org/ Center for Genomic Epidemiology ( 30 , – 32 ) Free Available at http://www.genomicepidemiology.org/ ; provides access to free tools related to genomic epidemiology (e.g., genome sequence typing or construction of phylogenetic trees) Desktop based CLC Genomics Workbench (CLC Bio, Aarhus, Denmark) Commercial Commercial desktop-based bioinformatics environments; may also provide support for integration with high-performance computing environments; often integrates existing free and open-source bioinformatics tools (e.g., Velvet for de novo assembly) BioNumerics (Applied Maths, Sint-Martens-Latem, Belgium) Commercial Ridom SeqSphere+ (Ridom GmbH, Münster, Germany) Commercial Open in a separate window List of bioinformatics analysis resources For any cloud-based solution, data privacy and security become a consideration.

Techniques: Construct, Software, Sequencing, RAST Test

Journal: Clinical Microbiology Reviews

Article Title: A Primer on Infectious Disease Bacterial Genomics

doi: 10.1128/CMR.00001-16

Figure Lengend Snippet: List of phylogenomics software a

Article Snippet: For those lacking resources or time for a local HTS data analysis environment, SaaS may be the preferred option so long as requisite analysis software is available to achieve project goals. table ft1 table-wrap mode="anchored" t5 TABLE 3 caption a7 Type Name Cost Comments Cloud services (IaaS/PaaS) Amazon Web Services (Amazon.com Inc., Seattle, WA, USA) Commercial Commercial cloud environments providing resources to construct customized high-performance computing environments; acts as a base from which additional software (e.g., Galaxy) can be utilized Microsoft Azure (Microsoft, Redmond, WA, USA) Commercial Google Cloud Platform (Google, Mountain View, CA, USA) Commercial Cloud services (SaaS) Illumina BaseSpace (San Diego, CA, USA) Commercial Commercial cloud-based bioinformatics analysis environments associated with different sequencing instruments; provides analysis tools and data management fine-tuned for each sequencing instrument; often integrates free and open-source bioinformatics tools described in this review (e.g., FastQC for quality control of sequence reads) Thermo Fisher Cloud (South San Francisco, CA, USA) Commercial Metrichor (Oxford, UK) Commercial DNAnexus (Mountain View, CA, USA) Commercial Cloud-based bioinformatics environment not specifically tied to any sequencing platform Web services Galaxy ( 24 ) Free Free and open-source bioinformatics analysis environment available at https://galaxyproject.org/ ; private instances can be installed on local hardware or within a cloud-based environment; RAST ( 29 ) Free Web service focused on genome annotation; available at http://rast.nmpdr.org/ Center for Genomic Epidemiology ( 30 , – 32 ) Free Available at http://www.genomicepidemiology.org/ ; provides access to free tools related to genomic epidemiology (e.g., genome sequence typing or construction of phylogenetic trees) Desktop based CLC Genomics Workbench (CLC Bio, Aarhus, Denmark) Commercial Commercial desktop-based bioinformatics environments; may also provide support for integration with high-performance computing environments; often integrates existing free and open-source bioinformatics tools (e.g., Velvet for de novo assembly) BioNumerics (Applied Maths, Sint-Martens-Latem, Belgium) Commercial Ridom SeqSphere+ (Ridom GmbH, Münster, Germany) Commercial Open in a separate window List of bioinformatics analysis resources For any cloud-based solution, data privacy and security become a consideration.

Techniques: Software, Variant Assay, Sequencing