Alfred

Alfred computes quality-control metrics and performs read- and haplotype-aware analyses for second- and third-generation sequencing data to support reliable downstream genomic analyses.

Key Features:

• Multi-sample, read-group-aware QC metrics: Computes read-group-aware, multi-sample metrics including GC bias, base composition, insert size, and sequencing coverage distributions.
• Haplotype-aware and allele-specific analysis: Performs haplotype-aware and allele-specific feature counting and annotation.
• Haplo-tagging of BAM/CRAM files: Supports haplo-tagging of BAM/CRAM files to enable haplotype-resolved analyses.
• Pipeline integration: Compatible with high-throughput sequencing pipelines for large-scale data processing.
• Support for multiple sequencing technologies: Handles assays from second- and third-generation sequencing platforms.

Scientific Applications:

• Genomics research: Provides QC and read-level analyses for genomics studies.
• Personalized medicine: Enables allele-specific and haplotype-resolved analyses relevant to clinical and personalized-medicine contexts.
• Large-scale sequencing projects and facilities: Facilitates quality monitoring across samples in DNA sequencing facilities and large-scale projects.
• Variant and haplotype-resolved studies: Supports detailed genetic variant analysis through haplotype-aware and allele-specific counting and annotation.

Methodology:

Computes read-group-aware QC metrics (GC bias, base composition, insert size, coverage distributions), performs haplotype-aware and allele-specific feature counting and annotation, and applies haplo-tagging to BAM/CRAM files.