Ecosyste.ms: Awesome
An open API service indexing awesome lists of open source software.
https://github.com/bbuchfink/diamond
Accelerated BLAST compatible local sequence aligner.
https://github.com/bbuchfink/diamond
sequence-alignment
Last synced: 30 days ago
JSON representation
Accelerated BLAST compatible local sequence aligner.
- Host: GitHub
- URL: https://github.com/bbuchfink/diamond
- Owner: bbuchfink
- License: gpl-3.0
- Created: 2015-03-10T23:19:00.000Z (over 9 years ago)
- Default Branch: master
- Last Pushed: 2024-09-07T19:20:24.000Z (2 months ago)
- Last Synced: 2024-09-27T04:23:20.070Z (about 1 month ago)
- Topics: sequence-alignment
- Language: C++
- Homepage:
- Size: 31.1 MB
- Stars: 1,030
- Watchers: 37
- Forks: 183
- Open Issues: 216
-
Metadata Files:
- Readme: README.md
- License: LICENSE
- Citation: CITATION.cff
Awesome Lists containing this project
- Awesome-Bioinformatics - DIAMOND - An ultrafast protein aligner for `blastp` and `blastx` like searches. [ [paper-2021](https://www.nature.com/articles/s41592-021-01101-x) ] (Next Generation Sequencing / Sequence Alignment)
README
Introduction
============
DIAMOND is a sequence aligner for protein and translated DNA searches,
designed for high performance analysis of big sequence data. The key
features are:
- Pairwise alignment of proteins and translated DNA at 100x-10,000x
speed of BLAST.
- [Protein clustering of up to tens of billions of proteins](https://github.com/bbuchfink/diamond/wiki/Clustering)
- Frameshift alignments for long read analysis.
- Low resource requirements and suitable for running on standard
desktops or laptops.
- Various output formats, including BLAST pairwise, tabular and XML,
as well as taxonomic classification.
[](https://github.com/bbuchfink/diamond/actions/workflows/cmake.yml)
[](https://travis-ci.com/github/bbuchfink/diamond)
[](https://github.com/bbuchfink/diamond/releases)
[](https://anaconda.org/bioconda/diamond)
[](https://anaconda.org/bioconda/diamond)
[](https://scholar.google.com/citations?user=kjPIF1cAAAAJ)
Documentation
=============
The online documentation is located at the [GitHub Wiki](https://github.com/bbuchfink/diamond/wiki).
Support
=======
Diamond is actively supported and developed software. Please use the [issue tracker](https://github.com/bbuchfink/diamond/issues) for malfunctions and the [GitHub discussions](https://github.com/bbuchfink/diamond/discussions) for questions, comments, feature requests, etc.
About
=====
Since 2019, DIAMOND is developed by Benjamin Buchfink at the Drost lab, Max Planck
Institute for Biology Tübingen. From 2018-2019, its development was supported by the
German Federal Ministry for Economic Affairs and Energy through an EXIST grant.
From 2016-2018, it was developed by Benjamin Buchfink as an independent researcher.
From 2013-2015, the initial version was developed by Benjamin Buchfink at the Huson lab,
University of Tübingen, Germany.
\[[:email:Email](mailto:[email protected])\]
\[[Twitter](https://twitter.com/bbuchfink)\] \[[Google
Scholar](https://scholar.google.de/citations?user=kjPIF1cAAAAJ)\]
\[[Drost lab](https://drostlab.com/)\]
\[[MPI-BIO](http://eb.tuebingen.mpg.de/)\]
**When using the tool in published research, please cite:**
- Buchfink B, Reuter K, Drost HG, \"Sensitive protein alignments at tree-of-life
scale using DIAMOND\", *Nature Methods* **18**, 366–368 (2021).
[doi:10.1038/s41592-021-01101-x](https://doi.org/10.1038/s41592-021-01101-x)
For sequence clustering:
- Buchfink B, Ashkenazy H, Reuter K, Kennedy JA, Drost HG, \"Sensitive clustering
of protein sequences at tree-of-life scale using DIAMOND DeepClust\", *bioRxiv*
2023.01.24.525373; doi: https://doi.org/10.1101/2023.01.24.525373
Original publication to cite DIAMOND until v0.9.25:
- Buchfink B, Xie C, Huson DH, \"Fast and sensitive protein alignment
using DIAMOND\", *Nature Methods* **12**, 59-60 (2015).
[doi:10.1038/nmeth.3176](https://doi.org/10.1038/nmeth.3176)