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.
yes | bash <(curl https://raw.githubusercontent.com/Clinical-Genomics/microSALT/master/install.sh)
cp configExample.json $HOME/.microSALT/config.json
vim $HOME/.microSALT/config.json
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.
microSALT analyse
contains functions to start sbatch job(s) & produce output tofolders['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.
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 )
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 - Various issues
- Maya Brandi - Various issues