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.
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For questions, help or feature requests please contact gear_genomics@embl.de
If you use Alfred in your work please cite:
Tobias Rausch, Markus Hsi-Yang Fritz, Jan O Korbel, Vladimir Benes.
Alfred: interactive multi-sample BAM alignment statistics, feature counting and feature annotation for long- and short-read sequencing. Bioinformatics. 2019 Jul 15;35(14):2489-2491.
https://doi.org/10.1093/bioinformatics/bty1007