mob-suite | Software tools for clustering , reconstruction and typing
kandi X-RAY | mob-suite Summary
kandi X-RAY | mob-suite Summary
mob-suite is a Python library. mob-suite has no bugs, it has no vulnerabilities, it has build file available, it has a Permissive License and it has low support. You can install using 'pip install mob-suite' or download it from GitHub, PyPI.
Plasmids are mobile genetic elements (MGEs), which allow for rapid evolution and adaption of bacteria to new niches through horizontal transmission of novel traits to different genetic backgrounds. The MOB-suite is designed to be a modular set of tools for the typing and reconstruction of plasmid sequences from WGS assemblies.
Plasmids are mobile genetic elements (MGEs), which allow for rapid evolution and adaption of bacteria to new niches through horizontal transmission of novel traits to different genetic backgrounds. The MOB-suite is designed to be a modular set of tools for the typing and reconstruction of plasmid sequences from WGS assemblies.
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mob-suite has a low active ecosystem.
It has 76 star(s) with 26 fork(s). There are 11 watchers for this library.
There were 1 major release(s) in the last 6 months.
There are 13 open issues and 99 have been closed. On average issues are closed in 160 days. There are no pull requests.
It has a neutral sentiment in the developer community.
The latest version of mob-suite is 3.1.8
Quality
mob-suite has 0 bugs and 0 code smells.
Security
mob-suite has no vulnerabilities reported, and its dependent libraries have no vulnerabilities reported.
mob-suite code analysis shows 0 unresolved vulnerabilities.
There are 0 security hotspots that need review.
License
mob-suite is licensed under the Apache-2.0 License. This license is Permissive.
Permissive licenses have the least restrictions, and you can use them in most projects.
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mob-suite releases are available to install and integrate.
Deployable package is available in PyPI.
Build file is available. You can build the component from source.
Installation instructions, examples and code snippets are available.
mob-suite saves you 1713 person hours of effort in developing the same functionality from scratch.
It has 3944 lines of code, 112 functions and 17 files.
It has high code complexity. Code complexity directly impacts maintainability of the code.
Top functions reviewed by kandi - BETA
kandi has reviewed mob-suite and discovered the below as its top functions. This is intended to give you an instant insight into mob-suite implemented functionality, and help decide if they suit your requirements.
- Assign contigs to clusters
- Filter out overlapping records that overlap with overlap_threshold
- Calculate hit coverage
- Calculate coverage scores for a reference sequence
- Perform clustering on clusters
- Calculate cluster score for each cluster
- Identify biomarkers
- Helper function to add the results of a recommarker
- Run blastn
- Fix the start of the blast index
- Build MOB - Typing report
- Generate host range information
- Parse command line arguments
- Validate arguments
- Generate host range for a host range
- Write MGE results to file
- Exclude overlapping records
- Updates the existing database
- Convert number to acs
- Run mash_distance on each cluster
- Check if the file has the given hashes
- BlAST a MGE
- Run MashSketch
- Unpack a tar archive
- Make a blastdb
- Argument parser
- Find genomes that match a MASH query
- Combine seqStats with user meta data
- Build cluster database
Get all kandi verified functions for this library.
mob-suite Key Features
No Key Features are available at this moment for mob-suite.
mob-suite Examples and Code Snippets
No Code Snippets are available at this moment for mob-suite.
Community Discussions
No Community Discussions are available at this moment for mob-suite.Refer to stack overflow page for discussions.
Community Discussions, Code Snippets contain sources that include Stack Exchange Network
Vulnerabilities
No vulnerabilities reported
Install mob-suite
We recommend MOB-Suite installation as a conda package due to large number of dependencies. The package is available through bioconda channel.
Support
James Robertson - james.robertson@canada.ca Kyrylo Bessonov - kyrylo.bessonov@canada.ca.
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