Omics Pipe

Omics Pipe automates multi-omics next-generation sequencing data analysis pipelines to enable reproducible processing and comparative analysis of large-scale datasets such as TCGA.

Key Features:

• Modular computational platform: Provides a modular framework for constructing and executing multi-omics workflows.
• Workflow automation: Automates execution of best-practice pipelines for next-generation sequencing analyses.
• Supported assays: Supports RNA-seq, miRNA-seq, Exome-seq, Whole-Genome sequencing, and ChIP-seq analyses.
• TCGA processing: Automates downloading and processing of TCGA samples for large-scale cohort analyses.
• Execution environments: Executes workflows on high-performance compute clusters and cloud environments.
• Reproducibility: Enhances reproducibility of complex bioinformatics analyses and generation of interpretable results.
• Large-scale dataset handling: Handles large cohorts, demonstrated on 100 TCGA breast invasive carcinoma paired tumor-normal datasets using UCSC hg19 RefSeq annotation.
• Reporting and aggregation: Produces comprehensive per-sample results reports and aggregates individual sample results to support comparative analyses with publications.

Scientific Applications:

• Transcriptomics: Analysis of RNA-seq and miRNA-seq data for expression profiling and differential expression studies.
• Variant discovery: Analysis of Exome-seq and Whole-Genome sequencing data for variant calling and cohort-level comparisons.
• Epigenomics: Analysis of ChIP-seq data for identification of protein-DNA interactions and regulatory regions.
• Cancer cohort analysis: Processing and comparative analysis of TCGA datasets, including paired tumor-normal studies and reanalysis with updated UCSC hg19 RefSeq annotation to identify overlaps and novel insights.

Methodology:

Automated downloading and processing of TCGA samples, execution of best-practice NGS workflows on high-throughput compute clusters and cloud environments, generation of comprehensive per-sample result reports, and aggregation of individual sample results for comparative analysis.