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.
Then continue with Configuration
bash <(curl https://raw.githubusercontent.com/Clinical-Genomics/microSALT/master/install.sh)
- Perform all steps under section 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 examples:
cp configExample.json $HOME/.microSALT/config.json
cp configExample.json /MY/FAV/FOLDER/config.json export MICROSALT_CONFIG=/MY/FAV/FOLDER/config.json
Then edit the fields to match your environment.
microSALT analysecontains 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 utilscontains various functionality, including adding manually new reference organisms and re-generating reports.
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.
microSALT will automatically download & use the resistance genes of resFinder (https://cge.cbs.dtu.dk/services/data.php). Any definitions will work, as long as they retain the same formatting.
- A slurm enabled HPC
- A (clarity) LIMS server
- Conda ( https://www.anaconda.com/distribution/ )
- Python 3.6
- sqLite Service ( https://www.sqlite.org/download.html )
Contributing to this repo
This repository follows the Github flow approach to adding updates. For more information, see https://guides.github.com/introduction/flow/
- Isak Sylvin - Lead developer
- Emma Sernstad - Accreditation ready reports
- Tanja Normark - Contamination analysis, various issues
- Maya Brandi - Various issues