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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.
module spider alfred to find out what environment modules are available for this application.
- HPC_ALFRED_DIR - installation directory
If you publish research that uses alfred you have to cite it as follows:
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