SeqWare

SeqWare manages scalable storage, querying, and analysis of large-scale next-generation sequencing (NGS) genomic variant data using HBase and Hadoop MapReduce to support variant annotation and performance profiling.

Key Features:

• Scalability and Performance: Built on HBase to handle petascale datasets and enable high-throughput storage and querying of thousands of genomes.
• Cloud-Based Infrastructure: Utilizes cloud computing technologies for dynamic allocation of computational resources for large-scale genomic processing.
• Hadoop MapReduce Integration: Incorporates Hadoop MapReduce for distributed data processing and performance profiling.
• Variant and Annotation Support: Stores and queries single nucleotide variations (SNVs), insertions/deletions (indels), translocations, and associated coverage and functional consequence annotations.
• NGS Data Compatibility: Designed specifically for data generated by next-generation sequencing technologies.
• Performance Profiling: Enables profiling of data-processing performance using real-world genomic datasets.

Scientific Applications:

• Genomic Data Management: Efficiently store and query large-scale genomic and whole-genome datasets.
• Variant Analysis: Perform detailed analysis of SNVs, indels, and translocations with coverage and functional consequence annotations.
• Biomedical and Clinical Genomics: Support genome resequencing studies and clinical analyses, including performance profiling and comparison of tumor/normal pairs such as glioblastoma multiforme.

Methodology:

Backend implemented on HBase (Apache Hadoop) with distributed data processing via Hadoop MapReduce and deployment on cloud computing infrastructure.