Awesome
<p align="center"> <img width="450" src="https://raw.githubusercontent.com/tobiasrausch/alfred/master/alfred.png"> <h1></h1> </p>
Alfred: BAM alignment statistics, feature counting and feature annotation
Alfred is available as a Bioconda package, as a pre-compiled statically linked binary from Alfred's github release page, as a singularity container SIF file or as a minimal Docker container. Please have a look at Alfred's documentation for any installation or usage questions.
Citation
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
License
Alfred is distributed under the BSD 3-Clause license. Consult the accompanying LICENSE file for more details.
Credits
HTSlib is heavily used for all alignment and VCF/BCF processing. Boost for various data structures and algorithms and Edlib for pairwise alignments using edit distance.