https://github.com/tobiasrausch/alfred

BAM Statistics, Feature Counting and Annotation
https://github.com/tobiasrausch/alfred

alfred alignment-metrics coverage-distribution feature-counting insert-size quality quality-control read-counts sequencing

Last synced: 6 months ago
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BAM Statistics, Feature Counting and Annotation

• Host: GitHub
• URL: https://github.com/tobiasrausch/alfred
• Owner: tobiasrausch
• License: bsd-3-clause
• Created: 2016-02-25T08:32:15.000Z (over 9 years ago)
• Default Branch: main
• Last Pushed: 2025-02-17T16:42:57.000Z (8 months ago)
• Last Synced: 2025-03-29T04:05:09.787Z (6 months ago)
• Topics: alfred, alignment-metrics, coverage-distribution, feature-counting, insert-size, quality, quality-control, read-counts, sequencing
• Language: C++
• Homepage: https://www.gear-genomics.com/alfred/
• Size: 21.9 MB
• Stars: 147
• Watchers: 9
• Forks: 12
• Open Issues: 4
• Metadata Files:
  • Readme: README.md
  • Contributing: CONTRIBUTING.md
  • License: LICENSE
  • Authors: AUTHORS

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## Alfred: BAM alignment statistics, feature counting and feature annotation

Alfred is available as a [Bioconda package](https://anaconda.org/bioconda/alfred), as a pre-compiled statically linked binary from [Alfred's github release page](https://github.com/tobiasrausch/alfred/releases/), as a singularity container [SIF file](https://github.com/tobiasrausch/alfred/releases/) or as a minimal [Docker container](https://hub.docker.com/r/trausch/alfred/). Please have a look at [Alfred's documentation](https://www.gear-genomics.com/docs/alfred/) for any installation or usage questions.

[Source Code](https://github.com/tobiasrausch/alfred/)

[Web Application](https://www.gear-genomics.com/alfred/)

[Documentation](https://www.gear-genomics.com/docs/alfred/)

## 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](https://doi.org/10.1093/bioinformatics/bty1007)

License

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Alfred is distributed under the BSD 3-Clause license. Consult the accompanying [LICENSE](https://github.com/tobiasrausch/alfred/blob/master/LICENSE) file for more details.

## Credits

[HTSlib](https://github.com/samtools/htslib) is heavily used for all alignment and VCF/BCF processing. [Boost](https://www.boost.org/) for various data structures and algorithms and [Edlib](https://github.com/Martinsos/edlib) for pairwise alignments using edit distance.