https://github.com/clinical-genomics/microsalt
Microbial Sequence Analysis and Loci-based Typing pipeline for use on NGS WGS data.
https://github.com/clinical-genomics/microsalt
clinical microbial pipeline resistance typing
Last synced: 10 months ago
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Microbial Sequence Analysis and Loci-based Typing pipeline for use on NGS WGS data.
- Host: GitHub
- URL: https://github.com/clinical-genomics/microsalt
- Owner: Clinical-Genomics
- License: gpl-3.0
- Created: 2017-10-12T12:38:03.000Z (over 8 years ago)
- Default Branch: master
- Last Pushed: 2024-12-16T04:08:20.000Z (over 1 year ago)
- Last Synced: 2024-12-16T05:19:50.385Z (over 1 year ago)
- Topics: clinical, microbial, pipeline, resistance, typing
- Language: Python
- Homepage:
- Size: 1.59 MB
- Stars: 2
- Watchers: 9
- Forks: 3
- Open Issues: 17
-
Metadata Files:
- Readme: README.md
- License: LICENSE
- Codeowners: .github/CODEOWNERS
Awesome Lists containing this project
README
[](https://github.com/clinical-genomics/microsalt/actions/workflows/run_tests.yml)
[](https://coveralls.io/github/Clinical-Genomics/microSALT?branch=master)
[](https://doi.org/10.5281/zenodo.4026043)
__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](https://pubmlst.org/databases). 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](https://bitbucket.org/genomicepidemiology/resfinder).
Any definitions will work, as long as they retain the same formatting.
## Requirements
### Hardware
- A [SLURM](https://slurm.schedmd.com) enabled HPC system
- A (clarity) LIMS server
### Software
- [Conda](https://conda.io)
- Python 3.6
- [SQLite](https://www.sqlite.org)
## 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