Atlas Suite

Atlas Suite performs integrated variant discovery and analysis for Whole Exome Capture Sequencing (WECS) data across SOLiD, Illumina, and Roche 454 platforms.

Key Features:

• Variant Calling: Includes Atlas-SNP2 for single nucleotide polymorphisms (SNPs) and Atlas-Indel2 for insertions and deletions (indels), enabling precise differentiation between true variants and sequencing or mapping errors.
• Statistical Models: Employs logistic regression models trained on validated whole-exome capture data, reported to achieve 96.7% sensitivity in variant detection.
• Platform Optimization: Optimized for Whole Exome Capture Sequencing (WECS) data generated on SOLiD, Illumina, and Roche 454 platforms.
• Integrative Pipeline: Provides an integrative pipeline for discovering genetic variants across supported next-generation sequencing platforms.
• User Customization: Allows adjustment of cutoffs to fine-tune variant filtering and calling thresholds.
• Genomic Database Integration: Supports integration with the Genboree Workbench and Genboree browser for incorporation of genomic databases.

Scientific Applications:

• Exome sequencing studies: Facilitates cost-effective discovery of variants in coding regions for studies of genetic contributions to disease and traits.
• Variant curation and functional genomics: Enables downstream curation and functional genomics analysis by integrating variant calls with genomic databases via the Genboree Workbench.

Methodology:

Variant calling is performed by Atlas-SNP2 and Atlas-Indel2; logistic regression models are trained on validated whole-exome capture sequencing data; supports integration of genomic databases within the Genboree browser.