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.
For questions, help or feature requests please contact firstname.lastname@example.org
Please cite Alfred's URL (https://gear.embl.de/alfred) in publications.