Science Score: 77.0%
This score indicates how likely this project is to be science-related based on various indicators:
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✓CITATION.cff file
Found CITATION.cff file -
✓codemeta.json file
Found codemeta.json file -
✓.zenodo.json file
Found .zenodo.json file -
✓DOI references
Found 8 DOI reference(s) in README -
✓Academic publication links
Links to: scholar.google -
✓Committers with academic emails
6 of 26 committers (23.1%) from academic institutions -
○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (12.3%) to scientific vocabulary
Keywords
Keywords from Contributors
Repository
Accelerated BLAST compatible local sequence aligner.
Basic Info
Statistics
- Stars: 1,169
- Watchers: 37
- Forks: 181
- Open Issues: 192
- Releases: 116
Topics
Metadata Files
README.md
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
- 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.
Documentation
The online documentation is located at the GitHub Wiki.
Support
DIAMOND is actively supported and developed software. Please use the issue tracker for malfunctions and the GitHub discussions for questions, comments, feature requests, etc.
About
DIAMOND is developed by Benjamin Buchfink at the Max Planck Institute for Biology Tübingen in collaboration with the Drost lab at the University of Dundee. 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] [X] [Bluesky] [LinkedIn] [Google Scholar] [Drost lab] [MPI-BIO]
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
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
Owner
- Name: Benjamin Buchfink
- Login: bbuchfink
- Kind: user
- Location: Tübingen, Germany
- Company: Max Planck Institute for Biology Tübingen
- Website: https://twitter.com/bbuchfink
- Twitter: bbuchfink
- Repositories: 1
- Profile: https://github.com/bbuchfink
Citation (CITATION.cff)
cff-version: "1.1.0"
authors:
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family-names: Buchfink
given-names: Benjamin
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family-names: Reuter
given-names: Klaus
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family-names: Drost
given-names: "Hajk-Georg"
date-released: 2021-04-07
doi: "10.1038/s41592-021-01101-x"
message: "If you use this software, please cite it using these metadata."
title: "Sensitive protein alignments at tree-of-life scale using DIAMOND"
version: "2.1.12"
GitHub Events
Total
- Create event: 3
- Release event: 3
- Issues event: 92
- Watch event: 125
- Delete event: 1
- Issue comment event: 198
- Push event: 21
- Pull request review comment event: 9
- Pull request review event: 7
- Pull request event: 18
- Gollum event: 40
- Fork event: 8
Last Year
- Create event: 3
- Release event: 3
- Issues event: 92
- Watch event: 125
- Delete event: 1
- Issue comment event: 198
- Push event: 21
- Pull request review comment event: 9
- Pull request review event: 7
- Pull request event: 18
- Gollum event: 40
- Fork event: 8
Committers
Last synced: 10 months ago
Top Committers
| Name | Commits | |
|---|---|---|
| Benjamin Buchfink | b****k@g****m | 1,723 |
| Klaus Reuter | k****r@m****e | 80 |
| Patrick Ettenhuber | p****r@g****m | 46 |
| yeahsmin | j****z@f****e | 23 |
| Joseph Mingrone | j****m@f****a | 5 |
| Kai Blin | k****n@b****k | 3 |
| Mahesh Madhav | 6****x | 3 |
| Simon Ye | m****l@y****m | 2 |
| Rui Chen | r****i@c****v | 2 |
| Michael R. Crusoe | c****e@d****g | 2 |
| Ben Fulton | b****n@i****u | 1 |
| Colin Brislawn | c****l@g****m | 1 |
| Daniel McDonald | m****t@c****u | 1 |
| Dr. K. D. Murray | 1****9 | 1 |
| Gabriel Leventhal | g****l@l****h | 1 |
| Jeff Yunes | j****f@y****s | 1 |
| Lee Bergstrand | l****y@g****m | 1 |
| Martin Larralde | m****e@e****e | 1 |
| Nathan Naveen | 4****n | 1 |
| Naveen | 1****n | 1 |
| Peter van Heusden | p****h@s****a | 1 |
| Steffen Möller | m****r@d****g | 1 |
| The Gitter Badger | b****r@g****m | 1 |
| gui-yue | y****i@g****m | 1 |
| snehring | s****g | 1 |
| Étienne Mollier | 6****r | 1 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 4 months ago
All Time
- Total issues: 233
- Total pull requests: 33
- Average time to close issues: 10 months
- Average time to close pull requests: 4 months
- Total issue authors: 177
- Total pull request authors: 21
- Average comments per issue: 3.83
- Average comments per pull request: 0.73
- Merged pull requests: 26
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 41
- Pull requests: 15
- Average time to close issues: 15 days
- Average time to close pull requests: 4 days
- Issue authors: 36
- Pull request authors: 6
- Average comments per issue: 1.32
- Average comments per pull request: 0.2
- Merged pull requests: 11
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- terrycojones (10)
- terancehhwong (4)
- xinehc (4)
- tseemann (3)
- ZeaMays14142 (3)
- katievigil (3)
- wwood (3)
- wdingx (3)
- raphenya (3)
- vagnerfonseca (3)
- Thernn88 (3)
- wmnwmn (3)
- Jehops (3)
- ilnamkang (2)
- RNAer (2)
Pull Request Authors
- heshpdx (9)
- kblin (3)
- kad-ecoli (2)
- nathannaveen (2)
- chenrui333 (2)
- emollier (2)
- prehensilecode (2)
- Gui-Yue (2)
- naveensrinivasan (2)
- muffato (2)
- colinbrislawn (1)
- wasade (1)
- Jehops (1)
- gaberoo (1)
- lucventurini (1)
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 1
- Total downloads: unknown
- Total dependent packages: 0
- Total dependent repositories: 0
- Total versions: 116
proxy.golang.org: github.com/bbuchfink/diamond
- Documentation: https://pkg.go.dev/github.com/bbuchfink/diamond#section-documentation
- License: gpl-3.0
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Latest release: v2.1.13+incompatible
published 6 months ago