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microsalt

Microbial Sequence Analysis and Loci-based Typing pipeline for use on NGS WGS data.

https://github.com/clinical-genomics/microsalt

Science Score: 49.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ○
    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ✓
    DOI references
    Found 3 DOI reference(s) in README
  • ✓
    Academic publication links
    Links to: zenodo.org
  • ○
    Committers with academic emails
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (15.3%) to scientific vocabulary

Keywords

clinical microbial pipeline resistance typing
Last synced: 6 months ago · JSON representation

Repository

Microbial Sequence Analysis and Loci-based Typing pipeline for use on NGS WGS data.

Basic Info
  • Host: GitHub
  • Owner: Clinical-Genomics
  • License: gpl-3.0
  • Language: Python
  • Default Branch: master
  • Homepage:
  • Size: 1.57 MB
Statistics
  • Stars: 2
  • Watchers: 8
  • Forks: 3
  • Open Issues: 18
  • Releases: 21
Topics
clinical microbial pipeline resistance typing
Created over 8 years ago · Last pushed 6 months ago
Metadata Files
Readme License Codeowners

README.md

Build status Coverage Status DOI

Microbial Sequence Analysis and Loci-based Typing pipeline

The microbial sequence analysis and loci-based typing pipeline (microSALT) is used to analyse microbial samples. It produces a quality control of the sample, determines a sample's organism specific sequence type, and its resistance pattern. microSALT also provides a database storage solution and report generation of these results.

microSALT uses a combination of python, sqLite and flask. Python is used for the majority of functionality, the database is handled through sqLite and the front-end is handled through flask. All analysis activity by microSALT requires a SLURM cluster.

Quick installation

  1. yes | bash <(curl https://raw.githubusercontent.com/Clinical-Genomics/microSALT/master/install.sh)
  2. cp configExample.json $HOME/.microSALT/config.json
  3. vim $HOME/.microSALT/config.json

Configuration

Copy the configuration file to microSALTs hidden home directory, or copy the configuration file anywhere and direct the envvar MICROSALT_CONFIG to it. See example:

cp configExample.json $HOME/.microSALT/config.json

or

cp configExample.json /MY/FAV/FOLDER/config.json export MICROSALT_CONFIG=/MY/FAV/FOLDER/config.json

Then edit the fields to match your environment.

Usage

  • microSALT analyse contains functions to start sbatch job(s) & produce output to folders['results']. Afterwards the parsed results are uploaded to the SQL back-end and produce reports (HTML), which are then automatically e-mailed to the user.
  • microSALT utils contains various functionality, including generating the sample description json, manually adding new reference organisms and re-generating reports.

Databases

MLST Definitions

microSALT will automatically download & use the MLST definitions for any organism on pubMLST. Other definitions may be used, as long as they retain the same format.

Resistance genes

microSALT will automatically download & use the resistance genes of ResFinder. Any definitions will work, as long as they retain the same formatting.

Requirements

Hardware

  • A SLURM enabled HPC system
  • A (clarity) LIMS server

Software

Contributing to this repo

This repository follows the Github flow approach to adding updates. For more information, see https://guides.github.com/introduction/flow/

Credits

  • Isak Sylvin - Lead developer
  • Emma Sernstad - Accreditation ready reports
  • Tanja Normark - Various issues
  • Maya Brandi - Various issues

Owner

  • Name: Clinical Genomics
  • Login: Clinical-Genomics
  • Kind: organization
  • Location: Stockholm, Sweden

GitHub Events

Total
  • Create event: 22
  • Release event: 6
  • Issues event: 11
  • Delete event: 7
  • Member event: 1
  • Issue comment event: 21
  • Push event: 160
  • Pull request review comment event: 26
  • Pull request review event: 30
  • Pull request event: 32
Last Year
  • Create event: 22
  • Release event: 6
  • Issues event: 11
  • Delete event: 7
  • Member event: 1
  • Issue comment event: 21
  • Push event: 160
  • Pull request review comment event: 26
  • Pull request review event: 30
  • Pull request event: 32

Committers

Last synced: over 2 years ago

All Time
  • Total Commits: 999
  • Total Committers: 25
  • Avg Commits per committer: 39.96
  • Development Distribution Score (DDS): 0.665
Past Year
  • Commits: 2
  • Committers: 2
  • Avg Commits per committer: 1.0
  • Development Distribution Score (DDS): 0.5
Top Committers
Name Email Commits
Isak Sylvin i****n@h****e 335
Isak Sylvin i****n@s****e 301
Isak Sylvin i****n@I****e 105
sylvinite i****n@o****m 94
sylvinite h****l@r****e 69
talnor t****k@s****e 20
henningonsbring h****g@g****m 19
Emma Sernstad e****d@s****e 11
i.sylvin@outlook.com s****e 9
Mropat m****t@g****m 6
Isak Sylvin i****n@i****e 4
Isak Sylvin i****n@1****e 4
Isak Sylvin i****n@I****l 4
Maya Brandi m****i@1****e 3
Isak Sylvin i****n@i****e 2
Maya Brandi m****i@1****l 2
Tanja Normark 3****r 2
Tanja Normark t****k@h****e 2
Daniel Backman d****n@s****e 1
Isak Sylvin i****n@1****e 1
Maya Brandi m****i@1****e 1
Isak Sylvin i****n@1****e 1
Kenny Billiau k****u@s****e 1
Anders Lind 6****y 1
Isak Sylvin i****n@1****e 1
Committer Domains (Top 20 + Academic)
scilifelab.se: 5 hasta.scilifelab.se: 2 130-229-7-143-dhcp.wlan.ki.se: 1 130-229-3-58-dhcp.wlan.ki.se: 1 130-229-12-24-dhcp.wlan.ki.se: 1 130-229-13-7-dhcp.wlan.ki.se: 1 isaksymb.ext.sll.se: 1 130-229-15-76-dhcp.wlan.ki.se: 1 130-229-5-21-dhcp.wlan.ki.se: 1 isaksymb.gaia.sll.se: 1 rastapopoulos.scilifelab.se: 1 isaksymb.scilifelab.se: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 61
  • Total pull requests: 102
  • Average time to close issues: about 1 year
  • Average time to close pull requests: 5 months
  • Total issue authors: 13
  • Total pull request authors: 13
  • Average comments per issue: 1.56
  • Average comments per pull request: 0.62
  • Merged pull requests: 79
  • Bot issues: 0
  • Bot pull requests: 2
Past Year
  • Issues: 8
  • Pull requests: 28
  • Average time to close issues: 29 days
  • Average time to close pull requests: 15 days
  • Issue authors: 4
  • Pull request authors: 3
  • Average comments per issue: 1.5
  • Average comments per pull request: 0.57
  • Merged pull requests: 23
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • sylvinite (17)
  • talnor (16)
  • samuell (5)
  • seallard (4)
  • henningonsbring (4)
  • karlnyr (3)
  • emmser (3)
  • Vince-janv (3)
  • moahaegglund (2)
  • patrikgrenfeldt (1)
  • beatrizsavinhas (1)
  • barrystokman (1)
  • eliottBo (1)
Pull Request Authors
  • sylvinite (42)
  • karlnyr (22)
  • samuell (15)
  • talnor (14)
  • ahdamin (5)
  • henningonsbring (4)
  • seallard (2)
  • dependabot[bot] (2)
  • b4ckm4n (1)
  • ingkebil (1)
  • Mropat (1)
  • AnnaLeinfelt (1)
  • Vince-janv (1)
Top Labels
Issue Labels
bug (13) Gain L (7) uSALT (7) KS requests (5) Effort L (5) Major (5) Effort M (4) Gain M (3) Urgency L (1) CG requests (1) Effort H (1) Gain H (1)
Pull Request Labels
dependencies (4)

Packages

  • Total packages: 1
  • Total downloads:
    • pypi 11 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 1
  • Total versions: 1
  • Total maintainers: 2
pypi.org: microsalt
  • Versions: 1
  • Dependent Packages: 0
  • Dependent Repositories: 1
  • Downloads: 11 Last month
Rankings
Dependent packages count: 10.0%
Forks count: 16.8%
Dependent repos count: 21.7%
Stargazers count: 27.8%
Average: 29.8%
Downloads: 72.8%
Maintainers (2)
sylvinite talnor
Last synced: 6 months ago

Dependencies

requirements-dev.txt pypi
  • black ==21.9b0 development
  • coverage ==5.5 development
  • gitlint ==0.15.1 development
  • mock ==4.0.3 development
  • pylint ==2.10.2 development
  • pytest ==6.2.5 development
  • pytest-cov ==2.12.1 development
  • python-coveralls ==2.9.3 development
  • yamllint ==1.26.3 development
requirements.txt pypi
  • biopython ==1.78
  • bs4 ==0.0.1
  • click ==7.1.2
  • flask ==1.1.2
  • flask_sqlalchemy ==2.4.4
  • genologics ==0.4.6
  • pymysql ==0.10.1
  • pyyaml ==5.4.1
  • sqlalchemy ==1.3.19
setup.py pypi
  • x.strip *