savR

savR parses and extracts sequencing run data from Illumina Sequence Analysis Viewer (SAV) files and generates quality control (QC) plots to assess sequencing experiment integrity.

Key Features:

• Parsing Capability: Interprets and extracts relevant information from Illumina SAV files containing detailed sequencing run data.
• Data Access: Provides programmatic access to raw sequence data and associated run metadata stored in Illumina SAV files.
• QC Plot Generation: Produces quality control (QC) plots for visualization and evaluation of sequencing performance.
• Bioconductor Integration: Integrates with the Bioconductor ecosystem to enable interoperability with other Bioconductor packages.

Scientific Applications:

• Genome assembly: Facilitates QC and data extraction steps required for genome assembly workflows.
• Variant calling: Supports quality assessment and data preparation for variant calling analyses.
• Transcriptome analysis: Enables QC-driven selection and inspection of sequencing data for transcriptome studies.
• Epigenetic studies: Provides sequencing quality assessment to support downstream epigenetic analyses.

Methodology:

Implemented in R and leveraging the Bioconductor project; integration with Bioconductor ensures interoperability with other Bioconductor packages.