Boiler

Boiler compresses collections of RNA sequencing (RNA-seq) alignments into compact representations that preserve a genomic coverage vector and empirical alignment distributions to reduce storage and support downstream analyses.

Key Features:

• Lossy compression: Retains only a genomic coverage vector and several empirical distributions while discarding most per-read information, producing a substantially reduced storage footprint.
• Per-read data recovery: Allows reconstruction of critical per-read information with only slight negative effects on downstream analyses such as isoform assembly and quantification.
• Fast querying: Enables rapid queries of compressed alignment data without requiring full decompression.

Scientific Applications:

• Large-scale RNA-seq data management: Storage-efficient management of extensive RNA-seq alignment collections for projects with high sequencing throughput.
• Transcriptome profiling: Preserves coverage information used in transcriptome profiling workflows.
• Differential gene expression studies: Supports differential gene expression analyses by retaining alignment summaries while minimizing storage requirements.
• Isoform discovery and quantification: Enables isoform discovery, assembly, and quantification workflows with minimal impact from compression.

Methodology:

Transforms raw RNA-seq alignment data into a compact representation by retaining a genomic coverage vector and empirical distributions that summarize alignments, discarding most per-read details, and storing a compressed format that permits querying without full decompression.