SV-plaudit

SV-plaudit generates visualizations of structural variant (SV) predictions and enables cloud-based curation to support validation and refinement of SV calls.

Key Features:

• Image Generation: Produces detailed images visualizing coverage and alignment signals from multiple samples for each predicted SV, representing the relevant genomic intervals.
• Cloud Integration: Automatically uploads generated images to a cloud framework for centralized storage and access.
• Data Compatibility: Accepts BAM and CRAM alignment files from Illumina paired-end sequencing, long-read sequencing from PacBio and Oxford Nanopore Technologies, and 10X Genomics linked-read data for image generation.
• Output Reports: Exports curation results as tab-delimited files and as annotated Variant Call Format (VCF) files.

Scientific Applications:

• Structural variant validation: Supports manual curation to improve the precision of SV calls from computational callers.
• High-throughput curation: Enables rapid review of large SV sets to facilitate scalable analyses in cohort and consortium studies.
• Genomic variation and disease studies: Aids investigation of SV contributions to genetic diversity and disease mechanisms by providing curated SV evidence.

Methodology:

Generates images from sequence alignments (BAM/CRAM, PacBio, Oxford Nanopore, 10X Genomics), uploads images to a cloud backend, and produces tab-delimited and annotated VCF outputs reflecting curation results.