https://github.com/bionf/xspect2
XspecT is a very fast, memory efficient and easy-to-use tool to taxonomically classify raw sequence-data, whole genome assemblies or metagenomes on the species and sub-species level
Science Score: 36.0%
This score indicates how likely this project is to be science-related based on various indicators:
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○CITATION.cff file
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✓codemeta.json file
Found codemeta.json file -
✓.zenodo.json file
Found .zenodo.json file -
○DOI references
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✓Academic publication links
Links to: arxiv.org -
○Academic email domains
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○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (15.0%) to scientific vocabulary
Repository
XspecT is a very fast, memory efficient and easy-to-use tool to taxonomically classify raw sequence-data, whole genome assemblies or metagenomes on the species and sub-species level
Basic Info
Statistics
- Stars: 0
- Watchers: 2
- Forks: 1
- Open Issues: 0
- Releases: 14
Metadata Files
README.md
XspecT
XspecT is a Python-based tool to taxonomically classify sequence-reads (or assembled genomes) on the species and/or MLST level using kmer indices and a Support Vector Machine.
XspecT utilizes the uniqueness of kmers and compares extracted kmers from the input-data to a kmer index. Probablistic data structures ensure a fast lookup in this process. For a final prediction, the results are classified using a Support Vector Machine.
The tool is available as a web-based application and as a command line interface.
Installation
To install XspecT, please download the lastest 64 bit Python version and install the package using pip:
pip install xspect
Please note that Windows and Alpine Linux are currently not supported.
Usage
Get the models
To download basic pre-trained models, you can use the built-in command:
xspect models download
Additional species models can be trained using:
xspect models train ncbi
How to run the web app
To run the web app, simply execute:
xspect web
This will start a local web server. You can access the web app by navigating to http://localhost:8000 in your web browser.
How to use the XspecT command line interface
To use the XspecT command line interface, execute xspect with the desired subcommand and parameters.
Example:
xspect classify species
If you do not provide the required parameters, the command line interface will prompt you for them.
For further instructions on how to use the command line interface, please refer to the documentation or execute:
xspect --help
Owner
- Name: BIONF
- Login: BIONF
- Kind: organization
- Repositories: 12
- Profile: https://github.com/BIONF
GitHub Events
Total
- Release event: 8
- Delete event: 1
- Push event: 41
- Pull request event: 29
- Fork event: 1
- Create event: 8
Last Year
- Release event: 8
- Delete event: 1
- Push event: 41
- Pull request event: 29
- Fork event: 1
- Create event: 8
Issues and Pull Requests
Last synced: 10 months ago
All Time
- Total issues: 0
- Total pull requests: 14
- Average time to close issues: N/A
- Average time to close pull requests: 1 day
- Total issue authors: 0
- Total pull request authors: 2
- Average comments per issue: 0
- Average comments per pull request: 0.0
- Merged pull requests: 10
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 0
- Pull requests: 14
- Average time to close issues: N/A
- Average time to close pull requests: 1 day
- Issue authors: 0
- Pull request authors: 2
- Average comments per issue: 0
- Average comments per pull request: 0.0
- Merged pull requests: 10
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
Pull Request Authors
- aromberg (19)
- Oemercetin06 (4)
Top Labels
Issue Labels
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Packages
- Total packages: 1
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Total downloads:
- pypi 250 last-month
- Total dependent packages: 0
- Total dependent repositories: 0
- Total versions: 17
- Total maintainers: 1
pypi.org: xspect
Tool to monitor and characterize pathogens using Bloom filters.
- Documentation: https://xspect.readthedocs.io/
- License: MIT License Copyright (c) 2020 w0rt0x Copyright (c) 2022 Dominik0304 Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
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Latest release: 0.5.4
published 11 months ago
Rankings
Maintainers (1)
Dependencies
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- H5py *
- Matplotlib *
- Psutil *
- Pympler *
- WTForms *
- Werkzeug *
- biopython *
- bitarray *
- click *
- loguru *
- mmh3 *
- numpy *
- pandas *
- requests *
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- wheel *
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