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metasbt

A scalable framework for automatically indexing microbial genomes and accurately characterizing metagenome-assembled genomes with Sequence Bloom Trees

https://github.com/cumbof/metasbt

Science Score: 57.0%

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  • ✓
    CITATION.cff file
    Found CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
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    .zenodo.json file
    Found .zenodo.json file
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    DOI references
    Found 1 DOI reference(s) in README
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    Scientific vocabulary similarity
    Low similarity (11.2%) to scientific vocabulary

Keywords

bioinformatics genomes metagenome-assembled-genomes metagenomics microbial-genomics sequence-bloom-trees
Last synced: 6 months ago · JSON representation ·

Repository

A scalable framework for automatically indexing microbial genomes and accurately characterizing metagenome-assembled genomes with Sequence Bloom Trees

Basic Info
  • Host: GitHub
  • Owner: cumbof
  • License: mit
  • Language: Python
  • Default Branch: main
  • Homepage:
  • Size: 805 KB
Statistics
  • Stars: 9
  • Watchers: 2
  • Forks: 3
  • Open Issues: 0
  • Releases: 4
Topics
bioinformatics genomes metagenome-assembled-genomes metagenomics microbial-genomics sequence-bloom-trees
Created almost 4 years ago · Last pushed 8 months ago
Metadata Files
Readme Changelog Contributing License Citation

README.md

MetaSBT

MetaSBT is a scalable framework designed to automatically index microbial genomes and accurately characterize metagenome-assembled genomes using Sequence Bloom Trees.

👉 Get started with MetaSBT by visiting our official wiki.

We also maintain a collection of public databases built with MetaSBT from curated sets of microbial genomes. You can explore and use them from the MetaSBT-DBs repository.

[!NOTE] Interested in using MetaSBT or our databases, or building your own private database but lack the necessary computational resources? Reach out to us! We’re always open to collaborations.

📖 Credits

If you use MetaSBT in your work, please cite:

bibtex @article{Cumbo2025.08.25.672238, author = {Cumbo, Fabio and Blankenberg, Daniel}, title = {Characterization of microbial dark matter at scale with MetaSBT and taxonomy-aware Sequence Bloom Trees}, journal = {bioRxiv}, year = {2025}, publisher = {Cold Spring Harbor Laboratory}, doi = {10.1101/2025.08.25.672238} }

🤝 Contributing

Long-term discussion and bug reports are maintained via GitHub Discussions and Issues, while code review is managed via GitHub Pull Requests.

Before contributing, please: 1. Check for existing issues or PRs related to your topic; 2. Write clear and concise titles and descriptions; 3. Include steps to reproduce bugs, relevant logs, version info, and other technical details when appropriate.

🛠️ Support

Need help?

Open an Issue or start a Discussion — we're happy to assist with any questions or technical problems.

Copyright © 2025 Fabio Cumbo, Daniel Blankenberg. See LICENSE for additional details.

Owner

  • Name: Fabio Cumbo
  • Login: cumbof
  • Kind: user
  • Location: Cleveland, OH, USA
  • Company: Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic

Ph.D. in Computer Science and Automation Engineering, Postdoctoral Research Fellow @BlankenbergLab, GMI, LRI, Cleveland Clinic, USA

Citation (CITATION.cff) 

cff-version: 1.2.0
message: "If you use this software, please cite it as below."
authors:
  - family-names: Cumbo
    given-names: Fabio
    orcid: https://orcid.org/0000-0003-2920-5838
  - family-names: Blankenberg
    given-names: Daniel
    orcid: https://orcid.org/0000-0002-6833-9049
title: "cumbof/MetaSBT: MetaSBT v0.1.5"
version: 0.1.5
date-released: 2025-06-27
url: https://github.com/cumbof/MetaSBT

GitHub Events

Total
  • Release event: 1
  • Watch event: 6
  • Delete event: 3
  • Push event: 25
  • Gollum event: 18
  • Create event: 1
Last Year
  • Release event: 1
  • Watch event: 6
  • Delete event: 3
  • Push event: 25
  • Gollum event: 18
  • Create event: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 0
  • Total pull requests: 1
  • Average time to close issues: N/A
  • Average time to close pull requests: 5 months
  • Total issue authors: 0
  • Total pull request authors: 1
  • Average comments per issue: 0
  • Average comments per pull request: 0.0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 0
  • Pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Issue authors: 0
  • Pull request authors: 0
  • Average comments per issue: 0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
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  • TrellixVulnTeam (1)
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Dependencies

metasbt/requirements.txt pypi
  • ncbi-genome-download >=0.3.1
  • ncbitax2lin >=2.3.2
  • numpy >=1.22.3
  • requests >=2.28.0
  • tqdm >=4.38.0
setup.py pypi
  • ncbi-genome-download *
  • ncbitax2lin *
  • numpy *
  • requests *
  • tqdm *