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https://github.com/bbuchfink/diamond

Accelerated BLAST compatible local sequence aligner.
https://github.com/bbuchfink/diamond

sequence-alignment

Last synced: 3 days ago
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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 (almost 10 years ago)
Default Branch: master
Last Pushed: 2025-01-16T20:04:32.000Z (10 days ago)
Last Synced: 2025-01-16T21:04:44.196Z (10 days ago)
Topics: sequence-alignment
Language: C++
Homepage:
Size: 31.2 MB
Stars: 1,089
Watchers: 38
Forks: 180
Open Issues: 194
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

        ![diamond](http://www.diamondsearch.org/diamond_white_95px.png)

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.

[![Build](https://github.com/bbuchfink/diamond/actions/workflows/cmake.yml/badge.svg)](https://github.com/bbuchfink/diamond/actions/workflows/cmake.yml)

[![image](https://img.shields.io/cirrus/github/bbuchfink/diamond)](https://cirrus-ci.com/github/bbuchfink/diamond/master)

[![image](https://img.shields.io/github/downloads/bbuchfink/diamond/total)](https://github.com/bbuchfink/diamond/releases)

[![image](https://anaconda.org/bioconda/diamond/badges/version.svg)](https://anaconda.org/bioconda/diamond)

[![image](https://anaconda.org/bioconda/diamond/badges/downloads.svg)](https://anaconda.org/bioconda/diamond)

[![image](https://img.shields.io/badge/dynamic/json?url=https%3A%2F%2Fraw.githubusercontent.com%2Fbbuchfink%2Fdiamond-data%2Frefs%2Fheads%2Fmain%2Fcitations.json&query=%24.citations&style=flat&label=Citations&color=%23a020f0

)](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

=====

DIAMOND is developed by Benjamin Buchfink. From 2019-2024, it was 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.

\[[:email:Email](mailto:[email protected])\]

\[[X](https://x.com/bbuchfink)\]

\[[Bluesky](https://bsky.app/profile/bbuchfink.bsky.social)\]

\[[LinkedIn](https://www.linkedin.com/in/benjamin-buchfink-875692105/)\]

\[[Google Scholar](https://scholar.google.de/citations?user=kjPIF1cAAAAJ)\]

\[[Drost lab](https://drostlab.com/)\]

\[[MPI-BIO](https://www.bio.mpg.de/)\]

**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)