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# Alfred: BAM Statistics, Feature Counting and Feature Annotation

Alfred is an efficient and versatile command-line application that computes multi-sample quality control metrics in a read-group aware manner. Alfred supports read counting, feature annotation and haplotype-resolved consensus computation using multiple sequence alignments. Alfred's companion web application enables interactive exploration of results. All code is open-source and hosted on Alfred's GitHub page.


  1. Installation
  2. Usage
  3. Web Application
  4. FAQ

For questions, help or feature requests please contact

Please cite Alfred's URL ( in publications.