rdeval

rdeval: Sequencing Read Metrics Evaluation and Reporting

rdeval computes and evaluates sequencing read metrics from FASTA (fa*), BAM, and CRAM files, supporting format conversion and quantitative assessment of read length, quality, and coverage for genomic datasets.

Key Features:

• Format Compatibility and Conversion: Supports FASTA (fa*), BAM, and CRAM formats with bidirectional conversion; enables comparison of compression efficiency and access performance between BAM and CRAM.
• High-Performance Metric Computation: Implemented in C++ for rapid calculation of sequencing read statistics; generates real-time metrics or compact snapshot files for downstream processing.
• Read Quality and Coverage Analytics: Quantifies read length distributions, sequencing quality metrics, and genome coverage across species and sequencing platforms.
• Automated Validation Workflow: Executes automated test workflows to ensure consistent computational accuracy across software updates.

Scientific Applications:

• Reference Genome Production: Evaluates read length, quality, and coverage improvements in high-quality genome assemblies, including applications in the Vertebrate Genomes Project (VGP) and long-read sequencing platforms such as PacBio.

Methodology:

rdeval processes sequencing read files (FASTA, BAM, CRAM) using C++-based algorithms to compute statistical metrics on read length, quality, and coverage. It supports on-the-fly computation or storage of metrics in snapshot files for efficient reuse and comparative analysis across datasets, species, and sequencing technologies.