ssvQC

ssvQC provides quality control and comparative analysis for enrichment-based NGS assays such as CUT&RUN, ChIP-seq, and ATAC-seq.

Key Features:

• Quality Control and Comparative Analysis: Performs comprehensive quality-control metrics and enables comparison of data quality across replicates and datasets.
• Support for Multiple Enrichment-Based Assays: Supports analysis of enrichment-based assays including CUT&RUN, ChIP-seq, and ATAC-seq.
• Evaluation of Fresh versus Frozen Samples: Includes workflows to compare CUT&RUN results from fresh and frozen cells to assess effects of sample preservation.
• Peak Calling and Replicate Analysis: Facilitates inspection of peak calling results and comparison across biological and technical replicates.
• Systematic Data Quality Reporting: Generates systematic QC summaries to report data quality for transcription factor binding and histone modification profiling studies.

Scientific Applications:

• Transcription Factor Binding Profiling: Supports genome-wide profiling and quality assessment of transcription factor binding datasets generated by CUT&RUN, ChIP-seq, or ATAC-seq.
• Histone Modification Profiling: Supports profiling and QC of histone modification datasets from enrichment-based assays.
• Protocol Optimization and Sample Preservation Assessment: Enables evaluation of experimental conditions such as fresh versus frozen sample use in CUT&RUN to inform protocol optimization.

Methodology:

Implemented in R; development involved comparing workflows using fresh and frozen samples in CUT&RUN experiments to produce a comprehensive QC pipeline.