TABLE 3.
List of bioinformatics analysis resources
| 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 |