Omic Analysis Platforms with Web-Based Interfaces and Cloud Support
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Basepair
Description / Purpose
BasePair is designed to run genomics, transcriptomics, and epigenetics analysis workflows. On this platform, raw sequence files are uploaded to Basepair for analysis using industry-standard workflows.
Specialization
DNA-seq, RNA-seq, ChIP-Seq, scRNA-Seq, ATAC-Seq. Interactive data visualizations enable user to find the genes or regions they are interested in and to generate publication-ready data graphs.
Features
- DNA-seq: Alignment, QC, Coverage, Genome/Variant Browser.
- RNA-seq: Alignment, QC, Read/Expression Counts, Genome Browser.
- ChIP-Seq Data: QC, Read Counts, Gene Bodies, TSS, Genome Browser.
- scRNA-Seq: QC, Normalization, Dimensionality Reduction, Clustering, DE Analysis.
- ATAC-Seq: Alignment, WC, Coverage, Genome/Variant Browser. Collaborative data sharing available, encrypted data security, and both technical and scientific support.
Supported Cloud Vendors
AWS-native service
Transferring between cloud vendors incurs additional fees.
Compliance
HIPAA, GDPR
Cost
Services are offered on two different plans: usage-based and annual licensing fees. Annual plan costs depend on the volume of data and features required. Basic plan charges typically range from $1,000–$2,000 annually.
Cancer Genomic Cloud (Velsera)
Description / Purpose
The Cancer Genomic Cloud platform on Velsera enables researchers to analyze large genomic datasets, facilitating discoveries in disease mechanisms and therapeutic approaches.
Specialization
Secondary analysis platform designed for cancer research.
Features
Over 800 tools and workflows are available, including germline and somatic variant calling, RNA-seq, Chip-seq, proteomics, imaging processing, etc. Collaborative data sharing allows the admin to control what project data each collaborator is allowed to access. Large datasets are available to include in analysis.
Supported Cloud Vendors
AWS-native service (default). Google Cloud and Microsoft Azure are also supported, but they are not native to the CGC and will incur additional transfer fees.
Transferring between cloud vendors incurs additional fees.
Compliance
HIPAA, FISMA Moderate, GxP, ISO 27001, NIST 800-53
Cost
Velsera operates on a pay-per-use model with additional licensing for enterprise clients. General access costs depend on the data storage and compute resources used on AWS.
DNAnexus
Description / Purpose
DNAnexus offers automation of data-intensive tasks and scalability. It supports a wide range of genomics applications, from research to clinical diagnostics.
Specialization
DNAnexus integrates large-scale genomic and multi-omics data analysis with clinical data. This platform also facilitates global data management, making it valuable for both research and clinical applications.
Features
NGS data analysis, translational informatics, population genomics. Applications are provided to visualize the data. This platform also supports AI/ML, cohort analysis, and JupyterLab notebooks. Collaborative data sharing is available.
Supported Cloud Vendors
AWS-native service, Microsoft Azure-native service, Google Cloud-native service.
Transferring between cloud vendors incurs additional fees.
Compliance
HIPAA, GDPR, FISMA Moderate, GxP, ISO 27001, ISO 13485
Cost
DNAnexus typically charges both for licensing and usage of cloud resources. Fees depend on the scale of data processed, storage, and specific compliance needs (e.g., HIPAA, GxP). For individual users or small labs, costs can range from $5,000–$25,000 per year for basic subscription plans.
DNASTAR Cloud
Description / Purpose
DNASTAR is a platform that facilitates genomic sequence assembly, alignment, and analysis. It provides a web-based platform for both primary and secondary genetic data analysis with a strong focus on user-friendliness.
Specialization
DNASTAR softwares include LASERGENE and NOVA. LASERGENE supports comprehensive sequence analysis for molecular biology, genomics, and proteomics projects. NOVA applications support protein modeling.
Features
Workflows provided on this platform are grouped into the following categories: molecular biology, protein analysis, genomics, and transcriptomics. Visual analysis of results is available and results can be exported as publication-ready images.
Supported Cloud Vendors
AWS-native service
Transferring between cloud vendors incurs additional fees.
Compliance
HIPAA, GDPR, ISO 27001
Cost
DNASTAR's academic cloud plans range from $300–$2,650 per year, depending on the user's features and storage requirements.
Galaxy Project
Description / Purpose
The Galaxy Project is a highly flexible and open-source web-based platform that can be deployed on AWS for genomic data analysis. It provides a user-friendly web interface where researchers can create and share workflows, analyze genetic data, and integrate various bioinformatics tools.
Specialization
Galaxy workflows are prepackaged in Docker images that can be deployed in the AWS cloud.
Features
Galaxy's Docker image workflows include the following analysis resources: genomics, metagenomics, transcriptomics, proteomics, and drug discovery. Tutorials and community support are available.
Supported Cloud Vendors
No native cloud services. Can be deployed on any cloud service, including AWS, Microsoft Azure, and Google Cloud.
Transferring between cloud vendors incurs additional fees.
Compliance
Compliance depends on how Galaxy is configured and deployed in the AWS cloud environment.
Cost
Galaxy is free and open-source. All fees are generated in the AWS cloud environment (ie cloud transferring, storing, and computing).
GenePattern
Description / Purpose
GenePattern is a suite of tools for genomic data analysis, including gene expression, proteomics, and other omics data. It is designed for ease of use.
Specialization
GenePattern enables users to create analysis pipelines and captures each version of the pipeline, including its methods, parameters, and data. This facilitates reproducibility which is critical in published research.
Features
Hundreds of analysis tools are provided, including RNA-seq, microarray, sequence variants and copy number variation, proteomics, flow cytometry, and gene networks. GenePattern also provides a Notebook environment that integrates texts, multimedia, executable code, and platform analyses into a single "research narrative" space that can be versioned and re-accessed.
Supported Cloud Vendors
No native cloud services. Can be deployed on AWS or Google Cloud.
Transferring between cloud vendors incurs additional fees.
Compliance
Compliance depends on how GenePattern is configured and deployed in the AWS cloud environment.
Cost
GenePattern is free and open-source. All fees are generated in the AWS cloud environment (ie cloud transferring, storing, and computing).
Illumina Connected Analytics and DRAGEN Bio-IT
Description / Purpose
Illumina Connected Analytics (ICA) platform is designed to manage, analyze, and interpret large volumes of multi-omics data in a secure, scalable, and flexible environment. This platform supports the integration with Illumina hardware and software, enabling users to build, customize, and version workflows. Illumina DRAGEN Bio-IT, a high-preformance NGS secondary analysis platform, can be used through ICA and includes comprehensive solutions for mapping, aligning, variant calling, and file compression.
Specialization
Designed for managing, analyzing, and interpreting large volumes of multi-omics data, ICA provides a flexible and scalable environment that integrates with Illumina's sequencing systems.
Features
Supports custom pipeline creation using Docker, Common Workflow Language (CWL), and Nextflow. Collaborative data sharing and data management available, as well as support for machine learning applications. Workflows are customizable and are adapted to process data generated with Illumina sequencing technology. Access is given to select scientfiic data and the Cohorts module enables molecular and clinical data exploration. Within ICA, DRAGEN Bio-IT supports rapid NGS secondary analysises of genome, exome, transcriptome, methylome, and cancer analysis. DRAGEN Bio-IT is capable of processing a 34x genome in ~30 minutes.
Supported Cloud Vendors
AWS-native service
Transferring between cloud vendors incurs additional fees.
Compliance
HIPAA, GDPR, ISO 27001. (Must be configured and used correctly)
Cost
Licensing fees are normally negotiated based on the size and needs of the institution, but pricing may be on the higher end due to the comprehensive analystic capabilities of this platform. AWS cloud analysis in ICA typically ranges from $5 - $20 per sample depending of the type of analysis.